Given that Sailor Pluto stands at the Door of Time, wouldn't she immediately recognize Usagi and co, when they were attempting to travel back through time? 

I never quite got how she seemed to be ignorant of who they were and nonetheless attacked them. After all, she knew of NQS, Mamoru, and the Inner senshi of Crystal Tokyo, so why respond that way?

Also, what was the deal with the Black Moon clan being able to travel through time without Pluto's agency? How'd that happen?

I think it was because nobody was ever supposed to approach the door of time, even though she did state she knew who they were before Chibiusa interrupted the would-be fight.

As for how the black moon was able to slip past her abilities, I'm not sure-though they probably got the ability to time travel from wiseman.

But we see NQS and King Endymion approaching it all the time. 

Was it just a matter of not allowing those from the past access to the future, or just her being super defensive?

How would Wiseman be able to manipulate time outside of Pluto's aid?

Cosmos-Hime wrote:

I think it was because nobody was ever supposed to approach the door of time, even though she did state she knew who they were before Chibiusa interrupted the would-be fight.

As for how the black moon was able to slip past her abilities, I'm not sure-though they probably got the ability to time travel from wiseman.

Agreed.