Clearly both of them are lying, the two of them have inconsistency on their speech, but the main reasons that made me side with the alik'r is:
- Why someone hidding from the thalmor would be working in the inn of Whiterun, the trade center of all Skyrim and a major target for the empire? Why not some small village near windhelm, where the empire and the thalmor have virtually non acess? The only ones that the guards will keep away from the city are the alikr's, not the thalmor.
- Why the dominion would send mercenary / assassins all the way from Hammerfell to capture ( or kill, like she said ) someone who spoke against the dominion? Hammerfell fought the dominion, so is probably still a lot of people there that still speak against them. Why the interest in this one person on the run? And why not hire some locals to do the job, some infiltrated agents like they usually do?
So, the most plausible cenario is that she indeed tried to sell hammerfell, tried to sabotage the resistance, and when they won the war and the peace treaty was sign, she run. Now they want her back.