It doesn't *change* anything, but you have no motivation to set Orpheus free, either.
Quite the opposite. On my first playthrough, I was really interested in exploring the githyanki questline, but frankly there is very little to discover about Orpheus as a character. Considering who Gith was, it remained an open question whether Orpheus is possibly the change Voss claimed he'd be, and whether it's even a good idea to free him.
On my Lae-free playthrough my character ended up in conflict with the emperor, so it was simply a matter of finding an alternative which would allow her to get rid of him.
In retrospect, I'd say Lae'zel and her questline mirror the issues with the main plot; there have been just too many changes, and it shows.
