I've been curious about this episode in Houston's life since I read a biography of him when I was young. I've read a few rumors as to why she left him, including that Houston was injured in combat and incapable of physically performing, but he had children later in life so that seems unlikely. Or that his wife loved another man, or that his youth living among the Cherokee was somehow repulsive her. I'm also curious about why it became such a scandal that he had to resign from government. Is there any good scholarship or speculation on this?
"Sam Houston" by James L. Haley covers this controversy pretty well in my opinion. Part of the problem in understanding what Eliza Allen was truly thinking is that she and her family destroyed most of the correspondence (and even pictures of Eliza).
I can't remember exactly what Haley contributes her leaving to (the exact reason is hotly debated because again there is no hard proof in correspondence), but Sam did have a pretty gnarly wound in his groin from the War of 1812 that remained open and seeped most of his life. It is possible this soured her, but Haley does mention she may have been in love with another man.
Now as far as this being a really scandalous thing in Tennessee has to do with rumors Eliza's family spread after she left him. The family felt they needed to spread rumors to save face after their daughter left a politically prominent man soon after marriage. Rumors included him being very distant and rude to her after the marriage.
Now Sam could have come out against these rumors and denounced Eliza and her family for tarnishing his good name but all indications show that he truly loved Eliza and was deeply wounded by her leaving. He refused to engage the rumors publicly and cast doubt on Eliza's reputation. He wrote several letters to her family trying to remedy the situation but nothing worked. Eventually his depression and subsequent deep drinking led him to resigning his governorship and heading off to rebuild his life.
Also, it is interesting to note that Sam was being groomed by Andrew Jackson to rise very high in Washington. It is not unlikely that he would have run for President of the U.S. one day (or at least made a try for a nomination) but the scandal and his deep depression ruined those chances.
edit: some wording but also to say I highly recommend Haley's work if you are interested in Sam Houston. Sam is truly one of the most interesting men of the period and if I could meet with any historical figure it would be Sam Houston.
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