In my own implementation I changed it so that it uses a way-point at every directional change the path would make.
That is a much, much safer way of doing it. Of course the negative effect is that it requires more way-points and thus sometimes exceeds the limit and thus doesn't fire the missile at all, where a clean-shot is possible.
I also found issues with the BAM_MISSILE-movement type itself when it comes to the path-finding in the first-place. It vastly changes how the path-finding works with some really unexpected results like making the path much longer (as it doesn't have to care about TUs) and flying through tiles with massive overlap like diagonal walls. In the sense of: Yes, it is theorethically possible the missile can pass through there, if it stays 100% on course. But the slightest deviation and it collides with something and goes boom way before reaching the target.
Using BAM_NORMAL with a MissileTarget-parameter and just changing that the missile-target itself is a valid tile in path-finding lead to much more desirable results in that regard. Basically returning a path wide enough for people to also take.
So having more restictions to how the waypoints for the blaster is set sounds like it would lead to fewer blaster-usages. And partially that is true as some shots are dismissed for requiring too many waypoints. But over the course of a mission more blasters were fired simply because the Aliens didn't blow each other up so much!