I think the whole idea behind the /weps commands is to be inclusive of all players so that they have a chance to use any weapon they want, similar to the cosmetics and hatpaints commands. For that reason, I do not think it should be removed, even if it means the occasional exploiter.
For exploiters, provided people have evidence in screenshot/video form, staff are able to issue bans on anyone caught exploiting the command, such as using the Atomizer - which gives you a double jump - in Deathrun, when double-jump as Scout is disabled in that gamemode.
Multiple accounts of exploitation from the same person means longer bans, so it's on them if they want to use a knowingly-banned weapon in a certain gamemode.
In my opinion, the real fix might be to make it more transparent about what weapons are banned on what gamemodes, to give players who may simply be experimenting with weapons a chance to avoid bans because of the exploit in question.
I've had a few people not know the Atomizer was banned on deathrun, whilst others clearly used it knowing it would give them an advantage, and had to ban them, some people on multiple occasions.
I think it would be better to let players play around with the /weps command rather than take away the command because we as a community are afraid of exploiters.