I think that would be a good thing to do.
I usually dont have a use for that crossbow, since i prefer bows, which are not that easy to get in this game.
I think the stats of it were slightly changed in the last patch too so it isnt as good as it was in previous version, one of the side effects is missing now. I may be wrong though.
Maybe it could have a one time use special effect applicable only to Alexander, which would be acceptable due to the story reasons.
Of course, if Zaleskar could check which weapon you are carrying when you talk to him with Ifan, and then produce that weapon as his story based assassination weapon that would be the best. But im not sure that kind of effort is necessary or such feature easily done...?
Maybe he could offer a one time special trading window with several items to choose from for free?
I would prefer is those other weapons you mention remain in the shop in case i need them for other characters.