So this proof seems to show that if ${\rm Isom}_S(X,F\times S)$ exists, then there is a base-change that trivializes $\pi:X\to S$. As a next step I would try to take multisections of ${\rm Isom}_S(X,F\times S)\to S$ to get a finite cover. You would probably want for each $s\in S$ a multisection that is unramified over $s$. That would give you s$ to get an étale local trivialization. If you are happy with a local trivialization in the Euclidean topology (assuming you're working over $\mathbb C$) then this should do it. For the issue of local trivialization in the Zariski topology, see below.
Finally, this proof definitely shows that if $F$ is projective with a finite automorphism group, then $\pi:X\to S$ is étale locally trivial: the projectivity of $F$ implies the existence of ${\rm Isom}_S(X,F\times S)$ and the finiteness of ${\rm Aut} F$ implies that ${\rm Isom}_S(X,F\times S)\to S$ is a finite étale morphism.
Addendum
Regarding the discussion of families that are analytically but not algebraically locally trivial, the important difference is whether they have a section or not.
If $\pi:X\to S$ is a smooth projective family without a section, then it cannot be algebraically locally trivial, since the closure of a section of the trivial part over a Zariski open set would give a section of the family. So, this way it is easy to find tons of examples.
On the other hand, a (quasi-)projective family will always have multisections, so it will have a section after a base change. So, for algebraically locally trivializing an isotrivial family the best hope is to do it after a finite base change. The above proof shows that if the appropriate $\mathscr Isom$ functor is representable by a quasi-projective scheme then this is doable. In particular, if $\pi:X\to S$ is projective, it can be trivialized with a finite base change (take a multisection of ${\rm Isom}_S(X,F\times S)\to S$).

