A work around for your issue at hand would be to use keyboard maestro (or any key mapper that could do as follow):
Create a condition:
if keystroke "cmd+v"
if app Remote Desktop at front
then keystroke ctrl + v
else cmd+v
It will take you current clipboard set by Alfred
I was able to test that when you do ctrl + v in a RDP, it will take into consideration the Alfred snippet you loaded in Mac clipboard, so my solution would work.