I think that is likely true once Stoner joined and HRC no longer wanted Dovi there but he insisted (not unreasonably imo) that his contract be enforced. I think it is far-fetched in regard to recent years prior to 2011 though, they may not have realised it in 2006, but by 2011 they knew Dani was a long shot to be riders' champion (hence signing Stoner), and Honda are also usually keen to win the manufacturers' title.
I also think there is absolutely no doubt Dovi is the inferior rider in general, look at their records as Jorge himself said, and I highly doubt Dovi is Jorge's superior if you put them both on a bike other than a Ducati last year. There was an interesting interview with Jorge pre-race, I think on Crashnet, where he says it took him so long to learn to ride the thing because it is so different, and needed to be ridden in a manner he considered illogical, which accords with what Stoner has said, that you had to ride the Ducati the way it wanted to be ridden. Dovi rode great last year and obviously Jorge looked horrible in comparison but it took Dovi 4 full years and part of a 5th to get there, it was a toss-up between keeping him and Iannone if you recall. They gave Jorge 1 season and a few races.
To me it looks as though they thought history had repeated and they had made the Rossi error again. It now appears they have repeated the Stoner error. Ducati make Jarvis look like a genius.