Yeah, we captured Santa Anna. So what?
We (as another poster put it) literally caught the Mexicans napping. About a third of Mexican forces in Texas were killed, wounded or captured, and of course we found Antonio Lopez de Santa Anna a day later, which gave us the leverage to get the other two-thirds of their forces headed back across the Rio Grande. Getting them back in theatre would require the usual huge undertakings to get an army going. That usually doesn't happen in the middle of a change of government.
While the Mexican government quickly deposed El Presidente and declared any treaties he'd signed with the Texan leadership null and void, without the military power to back up those claims available in theatre, they really couldn't do much about it.
There were actually quite a few states rebelling against Santa Anna's seizure of power at the time (some probably larger), the other rebellions got crushed. Fortunately, by the time Mexico was stable enough to consider taking Texas back, it was recognized by two foreign powers not exactly amenable to Mexican interests: the US and France.