I'm pretty sure that the hack checks only check the Pokemon in your party, but yes, you should be fine as long as you release the Latios. To get Pokemon off of Pokecheck without a ribbon, you need to download the Pokemon as a .pkm file and upload it to another fake GTS like Pokemon Selector or IR GTS.
That said, I'd be happy to clone it myself and trade you a copy sometime this weekend. Infact, I should have a Timid Latios ready by then too if you'd prefer that.