I was just looking in my guide that it is part of the railroad faction questline. I have yet to meet them and I've already explored and cleared it out will that break the quest?
Also I like Piper but I know she hates the institute. So would she like it if I ally with the railroad?

Railroad? This is a great game. I am level 28 atm, and have not heard of the Railroad. Did a tiny portion of the MQ, and lots of MM stuff, and a tiny bit of BoS stuff. Still haven't met anyone from Railroad or Institute. As far as I know, anyway!

I, too, have cleared out Corvega. I am now waiting to hear responses to your question, right along with you!

no guys it won't break the quests, i've already cleared the factory twice, once early on when i happened to randomley cruise and later on i went back to get the bobblehead and the enemies respawn there so i had to fight em all over again [which was fun] so no it won't ruin the quests.

It may have subtle influences, though --- I've run across letters on terminals in two ~different~ raider camps that mention the Corvega raider base and they both note that that base was taken out (by me, they do not state explicitly).... so presumably if you were to visit these other raiders BEFORE going to Corvega, you could get a hint about a raider base there, and the personalities involved , etc. before it was "taken out" (by you).

What about Piper? Will she like or dislike you allying with the Railroad?

Think you'll be okay, she's desperate for some sausage and gets all hot and flustered when she sees you jimmying a bobby pin into a lock