Actually, I took Sam's wary reaction as justifiable concern over the possibility of alien tampering. I can imagine her first concern would have been the possibility of tampering by a renegade Asgard (Loki), if they hadn't supposedly all been destroyed, and then the possibility of tampering by one of the more meddlesome of the ascended Ancients (despite their protestations that they're not allowed to meddle).

On the flip side, I can see where someone who is unfamiliar with Stargate canon coming to the conclusion that Sam is simply jealous of Rory.

Edited to add: Yes! I'm really looking forward to that conversation between Sam and John! He's definitely going to have some 'splainin' to do as to how he knows so much and I really don't envy him having to explain and apologize to Rodney eventually. *whistles*