No one is forcing you to play Foundry missions. There's a lot of things I don't do in STO. I don't do the Borg STFs, I don't PvP etc. If you aren't interested in playing a story oriented mission then you don't have to play it. Do what interests you.
If you want to shoot stuff that's fine I like to as well. Whenever the Mirror Event is active I grab a couple friends and we pew pew mirror ships for a while.