There's no proof about Francisco de Asís's homosexuality, although it is true that he was very close with Meneses, and in Paris they lived together. However, in Paris he also had a relationship with a female opera singer (sorry can't remember the name right now, I'll look it up afterwards...) with whom he exchanged very mmm... "hot" letters. So, at least, he was bisexual.
The failure in their marriage wasn't only due to Francisco de Asís, they weren't just fit for each other and neither of them had the character to face the facts and make the most of it. The marriage was indeed consumated and around 1847-1849 they had happy times. Two sons were born and died just after the birth in 1849 and 1850 and those were most probably Francisco's. About the rest, we can only conjecture, because no one can be sure unless a DNA test is made on their rests. So oficially, they still are Francisco's, as he acknowledged them. I wish those tests could be done!!