We know that at the end of high school, Willow was being headhunted for her computer expertise. What if the reason she didn't run off and join the NSA or go the Oxford was less to do with staying around Buffy and more to do with having been recruited into the Initiative. 

She works for them as a scientist. I can't imagine this being a problem for her. Although she might disagree with her superiors who insist that vampires and demons aren't sentient, she does think that they don't deserve to die and can't feel without a soul so what does it matter if they are cut up and experimented on.

We know that she doesn't have many classes with Buffy, so disappearing for hours at a time for 'study groups' is not going to ring any alarm bells. 

What happens when Spike is brought in - does she see him? Does he see her? Does it affect his choice to go to the Scoobies for help? Does he hide out in Revello Drive, waiting for Joyce to return and get found by Buffy?

What are the implications of Willow's involvement in the Initiative to her friendship with the Slayer? Does she inadvertently give too much away to Walsh (trying to impress her boss with her massive knowledge of demons and the occult) and set them after Buffy? What happens when they bring in a werewolf? Is it Oz? Veruca? and if so, is she feeling vindictive because of Oz's drifting attentions and therefore does nothing?

Does knowing that Riley is in the Initiative and effectively her boss make her less likely to encourage Buffy to get into a relationship with him? Does she ever go to the Wicca group and meet Tara? If not, does Tara find her way into the group in some other way?

Is there still a Will be Done spell? 

What changes that makes Buffy and Spike have to work together? How do they eventually accept their feelings for each other?

Bonus points if there is a mention of Willow being rabidly against animal testing. Because who would want to imagine the cute fluffy animals getting hurt?