Should I pre-cook sausages before scrambling into eggs? I have some fresh longaniza, maybe about 1 1/4" thick. Normally I'd throw them in the oven for 30-40 minutes or so then fry them real quick for texture.

I want to skin them, mash them, then mix them in with scrambled eggs or omelettes.

In terms of safety, should I still bake them before preparing them? Or mash them up raw and fry them for a while before adding the eggs? Or can I just throw the raw meat and eggs in the pan all at once?

They'll start cold, going from the fridge (~38F) to the oven/pan.
It takes more heat/time to safely cook sausage than it does to fully cook eggs. This would be especially true for omelettes, where the egg is in contact with the hot pan, and the filling only warms indirectly. Add your expectation to start with cold sausage, and cooking the sausage and egg at the same time seems like a really bad idea. (Yes, you could just cook the whole assembly longer, but you'd end up with seriously vulcanized eggs.)

Be safe: cook the sausage, and then add the eggs.