I wouldn't retire his number. As great of a guy Capirossi has been (Suzuki might argue otherwise), and as successful as he's been in lower classes and winning some premier class races (some may say he was deserving of a four-stroke Honda in 2002, which could have led him to another level of success, but I digress), he's never won a 500cc/MotoGP World Championship. My opinion is that numbers should be retired to riders killed on track, and absolute legends. I'm talking multiple world-championship-winning riders like Rossi, Doohan, Rainey, etc. Because if this precedent is set, then as Woody said, you can absolutely make the case that in addition to retiring the 46 when Rossi is gone (and looking likely the 27, as well), you now have to retire the 69, the 99, and the 26. Those three have achieved more than Capirossi in their careers, so there's no reason not to retire those numbers now.
When speaking about retiring numbers, I think you have to be extremely selective and careful about who you retire. I wouldn't have retired Hayden's 69, but with the Capirossi news, the numbers would suggest Hayden's has to be. It's a bad move, in my opinion.