You seem to be forgetting. Gaara's control over sand is based on how much chakra he has - and if his fights thusfar have been any notion, he still has a tendancy to run out rather quickly.
On top of this, his control has only extended over regular sand, and the 'living sand' which is a part of him, or an extension of himself. Gaara's control does not reach to other forms of 'living sand' - of which Crocodile is entirely consisting of. Furthermore, Crocodile's control over sand is almost, if possibly entirely, limitless, as is his ability to control his own body.
With that in mind, Gaara COULD attempt to take control of Crocodile's sand-body, but that would actually require a great deal of effort on his part. Effort that would eventually leave him drained of chakra and unable to fight properly. Crocodile, on the other hand, has no such handicap - as thus, his victory is assured.