I really doubt that a full annexation of Mexico was ever in the cards during the Mexican-American War. As you stated, the Whigs were hostile to the war to begin with, and were opposed to taking as much territory as the US got in OTL.
Also, you have to bring the racial attitudes of the time into play. Most of the territory the United States gained was sparcely populated to begin with. If they had taken much of Mexico-proper, than the US would also have inherited a population of Mexicans who were not seen as White, who didn't even speak English and, worse of all, were Catholics! Also, as this is not the Decades of Darkness timeline, those same Mexicans would eventually be allowed to vote, when the new territories became states.
I do think that it would have been possible to take more territory, however. I could certainly see the Baja California as well as Sonora, Chihuahau and possibly (possibly!) Coahuila. These regions were also less populated, although not so much as we find in the territories the US actually annexed. Although much of the land is desert, there might have been regions which were open to cotton plantings, and I do believe that there was silver there as well.
But you still have to deal with a strong Whig opposition and, likely, the growing concerns of Northerners about adding so much territory which is likely to eventually become slave states (and the fact that slavery was very unpopular amognst the Mexican population, which may bring in a whole slew of other problems).