There was a character in the Foundation
series that comes to mind, Harla Branno
. May be worth a few minutes to just search for a 'net copy of Foundation's Edge
and make a search for "Branno", just to have a quick glance at the quotes. Most of them won't make sense out of context, but there should be some good inspiration in there about how a master politician should talk or act like.
Anyway, she does not need to be an actual racist (only a practical one).
She may genuinely believe that she is working for the sake of the people. And why shouldn't she? You said that fantastic racism is prevalent, and those are the people who have elected her, and whom she has chosen to represent. She may be justified to think that humans would not be able to coexist with other races (and may even believe that the humans' nature is to blame for this, rather than the aliens' - but since she is representing the humans, it's their problem that she must solve). She could even lament the situation, insist that she has no personal grudge against the aliens, and bring it up at every possible occassion that she does not want the hero to mistake her for some sort of fanatic. How to account for it to her conscience is a different question - personal feelings should not sweep into a decision about what is the correct thing to do. She knows that she will hate herself for it later, but it was still the right thing. (But then again, does the hero, feel no responsibility for those children and grandchildren who will come after him, who will feel the consequences of their decisions -or lack of a decision- now?)
Even better if she is right. Or at least partially right, or one can leave the answer intentionally ambigious. You can give her some in-story justification for thinking that she is. If she has been such a successful politician as she probably is, she has probably had solved important public issues and had major successes that are telling her -and us- that with her methods she's on the right track. Some of the problems she wants to solve her may be things that the hero actually encounters in -some- form. (If you don't want these to be too negative, she can assure him that these are far bigger than what his limited experiences can reveal and that he has only seen the tip of the iceberg.)
The question is, if feel like you can pull off intelligent, insightful reasoning (even when it means doing something radical)? The hero does not neccessarily have to be more idealistic than her (with a more intimitate closeness to the aliens -I assume- he may have had entirely different experiences and revelations about what aliens are truly like), but her argument has to be sound and the correct ones in her position. The fact that she is something of a politician helps a little - she should already be used to making hard or unpopular choices. I think we can establish that she is not a romantic, and likely considers the hero naive for pursuing those views that, in her more experienced view, are unrealistic. She may even sympathize with him, just think that he can't form adequate judgement if he never had to make a hard decision when there was no good solution like she had to, or seeing the whole picture.
Lot of text, I hope that some of it helps a little.