I'm gonna go with option #2. Just cause the war is over, doesn't mean that the government would be any less paranoid in the aftermath. If fact, they'd likely over react, hoping to want help and get as much of an edge they can over this whole new enemy that came out of no where. Even with the Andalites coming to aid Earth, it wouldn't ease the situation any further. The Andalites weren't saints, and unlike the Animorphs learning of this the hard way, I doubt that the government would be as trusting as them in the first place. Suspicions would arise of the Andalites visiting Earth afterwards.
Afterall, the planet just got invaded by an nearly invisible enemy, do you really think it seems logical that they would automatically trust the next alien species that came along? The government would try to list the help of the Animorphs (covert ops, gathering information,.. whatever), and I don't see Rachel turning down an offer like that either. In fact, I can see Tobias joining her also.