Do you do much saluaging or mapping the downtown DC ruins before the increase in Enclave activity after turning on the purifier?

I usually do but I am starting to second guess if that is a good idea and wondering if I'm messing up the story.

EDIT: I put this question in the spoiler section on purpose so spoil away.

If the Enclave are NOT present in your current game, you can visit the purifier without consequence.

If the Enclave ARE present in your game, do your exploration first as the second trip will end your game (negated if you have Broken Steel installed).

No quests interfere with the main story, so you can do them however you want. Fallout 3 is about exploration as the story is just a means to get you out into the Capital Wasteland.

There are a few essential characters you can't kill, so don't worry about who you shoot.