If you look at the relevant premises and conclusions involved in a logically valid* argument against homosexuality:
A] Premise: Some fraction of the human population has a natural tendency to be homosexual.
B] Premise: Being homosexual is a moral wrong.
C] Conclusion: From A and B, we know that we should attempt to curb the natural tendency towards homosexuality.
then it should be fairly clear where my objection lies. I disagree with the second premise, "Being homosexual is a moral wrong." This argument is valid, as C logically follows if you accept A and B as true, but it is not sound to me, as I do not accept B as being true. If I were later convinced that B was true and that homosexuality was wrong, then I would have to accept the perscriptive statements in C as being true and sound as well.
If we take a look at an invalid argument in favour of permitting homosexuality:
F] Premise: Some fraction of the human population has a natural tendency to be homosexual.
G] Conclusion: It is wrong to try to change people who are homosexual into being heterosexual.
then your disagreement would be valid. Or, at least it would, if I were making this argument, instead of disagreeing with the validity of premise B in the first argument. My line of argument is roughly as follows:
X] Premise: Homosexuality is NOT a moral wrong.
Y] Premise: It acceptable to forbid an action
if and only if it is a moral wrong to do so.
Z] Conclusion: From X and Y, we know that it is NOT acceptable to forbid homosexuality.
which, as you can see, contains no claims about if it is natural or not to be homosexual. That fact is irrelevant to the question of if it is acceptable to be homosexual or not.
E:
If we take Leafsnail's additional premise "And you can't easily change it", formalize it and add it to the first argument, we get the following:
A] Premise: Some fraction of the human population has a natural tendency to be homosexual.
B] Premise: Being homosexual is a moral wrong.
C] Conclusion: From A and B, we know that we should attempt to curb the natural tendency towards homosexuality.
D] Premise: It is difficult to attempt to curb the natural tendency towards homosexuality.
E] Conclusion: From C and D, we know that it is acceptable not to attempt to curb the natural tendency towards homosexuality.
Which obviously falls appart unless you assume an additional premise of "It is acceptable to fail to do things that are proscribed morality if they are difficult to do." which, I rather doubt that many people would be willing to accept as a formal premise in their ethical system.
*Valid =/= True =/= Sound. See
http://tvtropes.org/pmwiki/pmwiki.php/Main/SoundValidTrue for definitions.