Greater autonomy != wanting to be annexed
True, but this fact also demonstrates that the majority of Crimeans weren't pro-Ukrainian, and as such gives more weight to the plentitude of anecdotal evidence that the majority of Crimea wanted to join Russia. Plus, it further complicates the "legality" of Crimean annexation by pointing out that Crimea had its constitution - which would've allowed it to join Russia on a 100% legal basis - forcibly rescinded by Kiyv a year after it was accepted.
Another point of view is that the Crimeans' desire to join Russia wasn't really that prevalent in the 90's, hence their support for Ukrainian independence, but rather arose during the years of Ukrainian corruption and mismanagement.
EDIT: Why haven't I noticed this before?
There are plenty of locals in the rebel's forces. Can't say that there are only Russians there.
Ah. In that case, the difference does change. Calling it an invasion does become... iffy, a bit. The only real justification would be because the rebels happen to be for Russia proper, so the "interest" in supporting rebels abroad is more-or-less a direct land-grab, which can only describe what the US has done to... well, usually small strategic islands or so. At least, I don't think any countries of the "West" has supported foreign rebels strictly so they could acquire the land.
I, personally, am of the theory that Russia really doesn't want that land, as evidence by the rebel high command being actively detrimental to the Novorossian war effort, instead, Putin was simply forced to help the rebels by the popular opinion, in order to uphold his image as "protector of Russian interests."