Well, Bezier curves are just polynomials, and interpolation with high degree polynomials has a bad reputation. It may be that the papers you're reading are just passing along the folklore. Experts whom I trust (Trefethen) say that the folklore is dubious -- the alleged problems are poorly articulated and the bad reputation is not deserved.
As one of the comments said, the numerical stability (or instability) depends on what particular computation you're doing. If you're doing interpolation, then you have to be careful what polynomial basis you use. The power basis is very bad; Bernstein and Chebyshev bases are much better.
The standard references in this area are two papers by Farouki and Rajan:
On the numerical condition of polynomials in Bernstein form
Computer Aided Geometric Design
Volume 4, Issue 3, November 1987, Pages 191-216
Algorithms for polynomials in Bernstein form
Computer Aided Geometric Design
Volume 5, Issue 1, June 1988, Pages 1-26
I don't see any problem in using Bezier control points as the independent variables in an optimization process. If you displace a control point by some vector $V$, then each point on the Bezier curve will move by $kV$, where $k \le 1$, since the Bernstein polynomials are $\le 1$ on the interval $[0,1]$. Seems like that's the sort of stability you're seeking.