You do need to get the no-CD FL exe file in order to play without your FL CD.
Some Freelancer features are hard-coded into the .EXE file, such as limits for visibility of some objects. Those features can be changed by a modder, but the no-CD.exe that you mention is just vanilla.
For example, using the no-CD version that you mentioned may make it impossible to see some features at long distance, that you are intended to be able to see in Crossfire, such as clues that might lead you to a jump gate or a wreck.
Also, I think that the launcher will try to overwrite your copy of Freelancer.exe.
So it is an excellent suggestion, but it may have a couple of drawbacks.