FreeDOS tries to be as compatible to MS-DOS as possible. So far, FreeDOS does a good job.
But a free and 100 % compatible implementation of LINK.EXE, which was shipped in MS-DOS 1.0 to 4.01 is still missing.
There are alternatives like WLINK.EXE from the Open Watcom C Compiler Suite available, but this linker is not 100% compatible with MS-DOS' LINK.EXE.
Rarely does anyone need a linker without a compiler. Most compilers come with their own linkers. We do have several 16-bit OMF linkers. Although none is 100% compatible in the most extreme cases, they do work for average use.
Some of the ones I've used recently (in small ways):
Warplink, JWlink, VAL, DJLink, ALink.
If there is specific functionality needed that is not supported here, I'm sure someone on the mailing list could point you in the right direction.