I think when Wesker came to after being knocked out of that window and saw that Jill was still alive (barely), a few things went through his mind.

1. Anger that she had managed to take him down

2. Impressed that she had managed to survive the fall

3. Desire for revenge on Chris and Jill

All of this culminated in the thought, “I should just take her with me.”

I mean he could have either left her for dead or go ahead and finish her off since that’s what everyone would believe. But, he decided to go to the trouble of getting her to safety and rebuild her strength. Of course this is Wesker we’re talking about so he did not do it out of the kindness of his heart. He worked with Jill and Chris for a few years. He knows them. He knows how important Jill and Chris are to one another (perhaps better than anyone).

Jill cares about Chris to the point that she would throw away her own life in order to save him. Chris has shown time and time again that he is incredibly driven to save those close to him (even if he isn’t always successful). The whole reason that Chris asked to go on the mission in Africa was because there was a chance to find out what happened to Jill.

So if you’re Wesker, wouldn’t it be handy if you could somehow turn the two major thorns in his side against one another? The last thing either of them would want to do is hurt or kill the other. So by brainwashing Jill, he could have an asset in that Jill is a formidable fighter in her own right (she defeated Nemesis after all) who could serve as an enforcer for those working under him and someone he could use to emotionally and physically torture Chris.

One thing in particular stood out to me, was that Jill acknowledged that she was conscious of her actions but was unable to resist his commands. It would have been simpler to drug her to the point where she would do whatever he said, but he clearly wanted her to be aware and to suffer through her actions. Wesker got the added bonus of torturing Jill by making her try to kill Chris.

In Wesker’s case, either he gets revenge by letting Jill be the one to kill Chris or by Chris having to kill Jill to save himself. It was clever to pit them against one another but it ultimately led to his downfall.