They're not the same species. They're not from the same planet. It should not be possible. Also, truthfully, it would be a very bad idea as a plot element.
You'd better make a better excuse. Because what you said does not make any sense. Daxamites and Kryptonians are basically of the same species and race, yes, with very few differences. It's as if Kara was from the US and Mo-el was from Canada. The differences are minimal. In addition, if Winn can date an alien (too ugly the creature, the purpose), I do not see why Kara and Mon-El, who has much more to do with the reasons already mentioned, could not be together and have a child of them. Also, I do not think it would ruin the show, but what is already being spoiled by a lot of sub-plots, these yes, totally meaningless.