You may be correct. I respect him and had relatives fight under him at San Jacinto. He worked hard to make sure that the first battle of the WBTS did not occur in Texas. The first encounter with actual bloodshed did occur in Texas though, but he was out of office by then.
Houston was for Texas, period. Here is an 1863 letter he wrote to Confederate General McGruder about driving the Federals out of Galveston:
General: It gives me great pleasure to mingle my congratulations with the many thousands that you have received. You, sir, have introduced a new era in Texas by driving from our soil a ruthless enemy. ... Your advent was scarcely known in Texas when we were awakened from our reverie to the realities of your splendid victory. Its planning and execution reflect additional glory on your former fame, as well as on the arms of Texas.Sam Houston, January 7, 1863.
"To secede from the Union and set up another government would cause war. If you go to war with the United States, you will never conquer her, as she has the money and the men. If she does not whip you by guns, powder, and steel, she will starve you to death. It will take the flower of the country-the young men."
"In the name of the constitution of Texas, which has been trampled upon, I refuse to take this oath (as governor of CSA Texas). I love Texas too well to bring civil strife and bloodshed upon her."
"I declare that civil war is inevitable and is near at hand. When it comes the descendants of the heros of Lexington and Bunker Hill will be found equal in patriotism, courage and heroic endurance with the descendants of the heroes of Cowpens and Yorktown. For this reason I predict the civil war which is now at hand will be stubborn and of long duration."