Is it best to keep to a lighter weight with isolation exercises in general?
No, you shouldn't be lowering the weight there out of fear. You should make sure your tendons are in order, and then treat it like any other exercise: Lift heavy and go hard.
In isolation exercises, you're using fewer muscle groups to perform the movement, so a natural effect of this is that you can't lift the same amount of weight here. Skullcrushers vs. bench press is a good example.
That said, you should still be challenging yourself weight-wise on isolation exercises, and not limiting yourself to weights that are far below your current potential. That is, if your goal is to increase strength in the muscle group in question.
I ended up with chronic tricep tendonitis/osis, I'm pretty sure the skullcrushers were the cause of it and I suspect I was going too heavy with them
I can't diagnose your elbow pain, but if you got tricep tendinitis that acting up during skullcrushers, I would postulate that the tendinitis was caused by something else, and simply flared up during skullcrushers.
The best treatment for tendinitis is to lay off it completely for a while, and come back slowly, so it can certainly be exacerbated by skullcrushers. But in general, this exercise shouldn't cause it, unless you're doing it absurdly often.