Just an FYI - The "Gate" was opened when El touched the monster in teh upside down. The most likely theory would be that the two dimensions were separate, and for the most part, neither would be aware of the other. Until a member of this dimension touched a member of the upside down and it became aware of the other dimension.
Much like in GOT where the white walkers were able to cross because Bran touched one of them in his vision.
I would suggest that the people at the lab were just doing whatever experiments they could and happened across the upside down where they discovered the presence of someone or something else. So, naturally, they pursued it. Once their actions caused the gate to open, they're really only concerned with one thing - covering their own asses. Not the good guys. The only time their actions would align with "good" would be out of pure coincidence when the right thing happens to be their own self preservation.