Even after her angry reaction towards Shepard's decision to work with Cerberus, Ashley sends him a mail apologizing for her outburst. In part, it reads:
I'm sorry for what I said back on Horizon. When I lost you two years ago, it tore me up. I prayed for you every day. I read a lot of Tennyson, thinking about you, just like I did when my dad passed. And then you came back, and it was like my prayers were answered. But I'm not who I was then, and neither are you.
I wouldn't have expected you to work for Cerberus, but I know why they sent you to Horizon. I saw how many people were lost there, and if anyone can stop the Collectors, you can. I can't go where you're going, but I can wish you luck.
Even so, she gives Shepard a very hard time on Mars, and in several exchanges between them you can try to convince Ashley that you did what you did for the good of the galaxy.
Shepard's also returned to working for the Alliance, and has more or less severed ties with Cerberus. It's pretty clear by the end of the Mars mission that Shepard is not on the best of terms with them.
I think taken as a whole, it's not too farfetched to conclude that Ashley's concerns about Shepard's temporary alliance with Cerberus have been overshadowed by Shepard's continual struggle against the Reaper threat.