The problem presented in the question consists of two coupled, nonlinear ODEs with three boundary conditions, two at the origin, and the third being that the solution asymptotically approaches a separatrix at infinity. The desired solution is rt (an eigenvalue) as a function of κ. The answer below shows, first, that the problem as stated in the question has no eigenvalues, due principally to an essential singularity at ηb[0] == 0. However, modifying the ηb[0] == 0 boundary condition to, for instance, ηb[0] == 7/10 (with an associated change to ηa[0]) does allow rt to be computed as a function of κ.
Analysis of question's ODE system
It is convenient to renormalize rt and τ to eliminate the extraneous constants α, β, and θ. With this transformation the ODEs become
eq1 = D[ηb[τ], τ] == (ηa[τ] - κ ηb[τ] Exp[1/( rt ηb[τ])]);
eq2 = D[ηa[τ], τ] == (-ηa[τ] + κ ηb[τ] Exp[1/( rt ηb[τ])] + δ (1 - ηa[τ]));
Their stationary solution at large τ is obtained by setting first derivatives to zero.
Equal @@@ Flatten@Solve[{eq1[[2]] == 0, eq2[[2]] == 0} /. κ ηb[τ] Exp[1/(rt ηb[τ])] -> z,
{ηa[τ], z}] /. z -> κ ηb[τ] Exp[1/( rt ηb[τ])]
(* {ηa[τ] == 1, E^(1/(rt ηb[τ])) κ ηb[τ] == 1} *)
The asymptotic expression for ηb[τ] is readily solved by
Reduce[κ ηb[τ] Exp[1/( rt ηb[τ])] == 1, ηb[τ], Reals] // FullSimplify
(* (ηb[τ] == E^ProductLog[-(κ/rt)]/κ && ((rt > 0 && ((κ > 0 && rt >= E κ) || κ < 0)) ||
(rt < 0 && ((rt <= E κ && κ < 0) || κ > 0)))) ||
(ηb[τ] == E^ProductLog[-1, -(κ/rt)]/κ && ((κ > 0 && rt >= E κ) ||
(rt <= E κ && κ < 0))) *)
Cases[%, Equal[ηb[τ], z_] -> z, Infinity];
Plot[Evaluate[% /. κ -> 1], {rt, -5, 5}, AxesLabel -> {rt/κ, κ ηb}]

(The blue curve corresponds to E^ProductLog[-(κ/rt)]/κ, and the orange curve to E^ProductLog[-1, -(κ/rt)]/κ.)
To determine whether the asymptotic solution corresponds to a separatrix (as desired by the OP) or an attractor, it is convenient to combine the two first-order ODEs into a single second-order ODE.
sub = Solve[{eq1, eq2}, {ηa[τ], D[ηa[τ], τ]}] // Flatten // Simplify
(* {ηa[τ] -> E^(1/(rt ηb[τ])) κ ηb[τ] + ηb'[τ],
ηa'[τ] -> δ - E^(1/(rt ηb[τ])) δ κ ηb[τ] - (1 + δ) ηb'[τ]} *)
eq = Equal @@ Simplify[Solve[D[eq1, τ] /. sub, ηb''[τ]][[1, 1]]]
(* ηb''[τ] == δ - E^(1/(rt ηb[τ])) δ κ ηb[τ] - (1 + δ + E^(1/(rt ηb[τ])) κ) ηb'[τ]
+ (E^(1/(rt ηb[τ])) κ ηb'[τ])/(rt ηb[τ]) *)
Now, linearize this ODE about the asymptotic solution for ηb[τ] (designated ηbm) and solve it in terms of Exp[k τ].
% /. Derivative[n_][zz_][τ] z_ :> Derivative[n][zz][τ] (z /. ηb[τ] -> ηbm);
Collect[Subtract @@ ((Series[%, {ηb[τ], ηbm, 1}] // Normal) /.
E^(1/(rt ηbm)) -> 1/(κ ηbm) /. ηb[τ] -> ηb[τ] + ηbm), {ηb''[τ], ηb'[τ], ηb[τ]}, Simplify];
sk = k /. Solve[(% /. {ηb''[τ] -> k^2 ηbm, ηb'[τ] -> k ηbm, ηb[τ] -> ηbm}) == 0, k]
(* {(-1 + 1/(rt ηbm) - ηbm - δ ηbm - Sqrt[-4 (δ - δ/(rt ηbm)) ηbm +
(1 - 1/(rt ηbm) + ηbm + δ ηbm)^2])/(2 ηbm),
(-1 + 1/(rt ηbm) - ηbm - δ ηbm + Sqrt[-4 (δ - δ/(rt ηbm)) ηbm +
(1 - 1/(rt ηbm) + ηbm + δ ηbm)^2])/(2 ηbm)} *)
Plots for positive κ are
GraphicsRow[Plot[Evaluate@Table[{sk /. ηbm -> E^ProductLog[-(κ/rt)]/κ,
sk /. ηbm -> E^ProductLog[-1, -(κ/rt)]/κ} /. {δ -> 1/100, κ -> κ0}, {κ0, 1, 5}],
{rt, -5, 5}, AxesLabel -> {rt, k}, PlotRange -> #, ImageSize -> Medium] &
/@ {{-6, 6}, {-.06, .06}}]

and for negative κ

Asymptotic solutions ηbm == ηb[τ] for which both values of k are negative are attractors, not separatrices. Thus, there are no separatrices for rt/κ < 0. However, for rt and κ both positive, E^(1/(rt ηb[τ])) is infinite at ηb[τ] == 0 (ηb[τ] must be positive in order to avoid integrating through ηb[τ] == 0 to reach ηbm), and the boundary condition cannot be satisfied. The same is true for rt and κ both negative. Consequently, no solutions satisfying the boundary conditions, including existence of a separatrix, exist. A typical solution including an attractor is
κ0 = 1; rt0 = -1;
c = z /. FindRoot[(κ z Exp[1/(rt z)] /. {κ -> κ0, rt -> rt0}) == 1, {z, 1}]
sol = Flatten@NDSolve[{eq1, eq2, ηa[0] == 1, ηb[0] == 1/10000} /. {κ -> κ0,
rt -> rt0}, {ηa[τ], ηb[τ], ηb'[τ]}, {τ, 0, 10000}, WorkingPrecision -> 30];
Show[LogLinearPlot[Evaluate[{ηa[τ], ηb[τ]} /. sol], {τ, 1/100, 10000}],
LogLinearPlot[{1, c}, {τ, 1/100, 10000}, PlotStyle -> Dashed]]

Eigenvalues for modified boundary conditions
Two conditions must be satisfied to obtain eigenvalues: There must be a separatrix, and it must be accessible from the τ == 0 boundary conditions of the ODEs. One revised set of boundary conditions accomplishing this (for rt and κ both positive)
ηa[0] == -(1/5) + 7/10 E^((10/7)/rt) κ;
ηb[0] == 7/10;
Solving the ODEs with these three boundary conditions is conveniently performed using the procedure described in question 140833. First, transform the second-order ODE to
eqw = eq /. {ηb''[τ] -> w'[x] w[x], ηb'[τ] -> w[x], ηb[τ] -> x}
(* w[x] w'[x] == δ - E^(1/(rt x)) x δ κ + (E^(1/(rt x)) κ w[x])/(rt x)
- (1 + δ + E^(1/(rt x)) κ) w[x] *)
with x ranging between ηbm and 7/10, w[ηbm] == 0, and w[7/10] == -1/5. This system can be solved by
sp[δ0_?NumericQ, κ0_?NumericQ, rt0_?NumericQ] :=
NDSolveValue[{eqw, w[xm + offset] == First@c offset} /.
xm -> E^ProductLog[-1, -(κ/rt)]/κ /. {δ -> δ0, κ -> κ0, rt -> rt0}, w[7/10],
{x, (E^ProductLog[-1, -(κ/rt)]/κ /. {κ -> κ0, rt -> rt0}) + offset, 7/10},
WorkingPrecision -> 26]
start = Rationalize[{{1/100, 1/2 - 5/100, rt /. FindRoot[sp[1/100, 1/2 - 5/100, rt]
== -1/5, {rt, 3/2}, WorkingPrecision -> 30, MaxIterations -> 1000]},
{1/100, 1/2 - 4/100, rt /. FindRoot[sp[1/100, 1/2 - 4/100, rt]
== -1/5, {rt, 3/2}, WorkingPrecision -> 30, MaxIterations -> 1000]}}, 0];
new = 1; i = 3;
While[new != 0 && i < 100, tem = 2 start[[i - 1]] - start[[i - 2]];
If[tem[[3]]/tem[[2]] < E, Break[]];
new = Rationalize[Check[rt /.
FindRoot[sp @@ ReplacePart[tem, 3 -> rt] == -1/5, {rt, Last@tem},
WorkingPrecision -> 30, MaxIterations -> 1000], 0], 0];
If[new != 0, AppendTo[start, Join[Most@tem, {new}]]]; i++]
ListPlot[Rest /@ start, AxesLabel -> {κ, rt}]

The upper bound on this curve is set by the requirement that rt/κ > E, so that the separatrix exists. It is possible to extend the curve to lower values of κ but only with rapidly increasing WorkingPrecision.
z Exp[1/(r z)]contains an essential singularity atz == 0. Are you sure the equations are correct? – bbgodfrey Mar 29 '16 at 13:31