Personally, I never view Ashley as racist and that is never the reason why I choose Kaidan over her. At best, she is ignorant but I get that her resentment was based on how she was being labelled as an 'alien sympathizer' in her entire life and in ME verse, humanity are still diverged about the alien issues (remember how popular Cerberus become and how many people willingly kill themselves for their cause) and people like Ashley are common... even Miranda and Jacob was distrusting with some of the alien crews you pick up and they merely view them as "asset to the team" rather than as people and they hardly interact with each other either.
For me, Garrus always struck me as the most bigoted of the crew, even more so than Ash. And yet, he never get labelled as a racist even though he is the one who is okay with genocide and the extinction of two species because they dared to defy the council. Everyone love to ignore how he aggravate Wrex purposely about how his people deserve the genophage TWICE and then later with Tali about how her people deserve being outcast and dying because they created the Geth. Then in ME3, he even whispered that he would take the Dalatrass deal if it wasn't his people that needed their help. Wrex is supposedly his buddy and if he had the chance, he would betray him because of his prejudice. I'm quite uncertain about why people would think a random comment about wondering if Keepers are aliens or animals as racist when we already have someone who justify the genocide of two species because they screwed up several hundreds years ago. Tolerance to genocide of any race is abhorrent and undeniably racist and is very real.
But its good that the writers did include them^ in the beginning but it was frustrating that this was being gloss over in the later installments because the character became favourites and they need people to buy they game. I don't think that was wrong for them but come on.. wouldn't it be nice if Garrus actually have a special scene at the Shroud, say the Dalatrass contacted him and he was the one who wanted to kill Mordin and Shepard had to guilt him out or let him or kill him. Potential drama....