Sure...every driver wants to be top dog, but I think he'd jump at a Ferrari seat regardless of who his teammate would be. They have a history of having strong pairings and showing they know how to handle them in an even-handed manner.
Besides, there's a big difference between (1)beng treated as an equal in a team and (2)being treated as a #2 to a rookie when you were signed as a #1 or at least as an equal.
I don't spend much time on F1 BBs so I am not familiar with what McLaren did to treat Alonso as a number 2, other than the fact that Lewis did out-perform Alonso during the first half of the season, a period of adjustment for Alonso in his new ride. By the time Alonso got up to speed, there was resentment already brewing.
Both drivers on the serious teams have their own mechanics and engineer so I find it hard to believe that given all the money they were giving Alonso they would give him the worst of the lot. However, it could be that when a team designs a car, they give it characteristics that might favour one driving style over another. I believe this was the case between Schumacher and Barrichello. The design, being hard to change during the season, would hamper one of the drivers for the whole year. Maybe the car was more suited to Hamilton than Alonso?
McLaren's most recent top-drivers pairing was the famous Senna-Prost feud. It has been a few years since. But IIRC, they were allowed to race each other. The personality of the driver came heavily into play in that war.
I agree that Alonso will make the jump to Ferrari, I just see him being paired with a clear, up-and-coming, #2 driver. Wasn't there a rumour of Senna's nephew driving for the scuderia?