Well, her thing is being indirect so it's going to be hard to tell, but:
Her antics seem to focus around keeping Gensokyo as an AREA going , rather than caring about the population (beyond Reimu, who needs to be kept alive, and possibly Yuyuko) .
You can't even say she is pro-youkai, since she has public acts of benevolence towards the humans, like appearing to fix issues like the missing household gods in the human village (Though she was resonsible for this), as well as 'rarely' attacking humans, which is pretty good by Touhou standards. She also organized a suicidal war of youkai against the Lunarians for the purposes of teaching them not to outstep their boundaries outside of Gensokyo.
Even her (fake) name "Yakumo" is told be be from a poem that is an allegory for Gensokyo- a mansion where one can live in peace, and a fortress to keep the gods trapped inside. Exactly why she wants to do this is uncertain, especially as she isn't formally in charge, and she is powerful enough to no have to care about Gensokyo.
She doesn't really appear in the smaller incidents or squabbles between people in Gensokyo, but she stoops cleans up the environment when junk comes through the barrier like that broken pylon.
However, just look at how much Kasen (Usually something of a moral authority figure) seems to hate Yukari- It's probably the second biggest fued in the series after Mokou+Kaguya. Yuakri too was evidently pissed when Sumireko and Kasen were messing around with the barrier.
It's sort of grey, really- she helps preserve the status quo, so if how Gensokyo currently works is good, then she could be. If (like Kasen) you have some doubts about this, then she's rotten and her ends do not justify her means