If a weapon has zero CND you can't equip it so you can't use your weapon repair kits.
I went to Old Lady Gibson thinking that I can "trick" her by removing almost all my bottlecaps from inventory, so when the repair menu appears she can fix just a fraction of it, enough so I can use my weapon repair kits...but no, you can only choose repair for the maximum repair available which is over 6000 caps in this case(broken sniper rifle from legionnaire assassin).

So, is there some other way to repair it?

I think it is very dumb that repairing NPCs can't fix weapons proportionately to your amount of caps instead of maximum repair.. :brokencomputer:

If I'm not mistaken and I may be since I've used an npc to repair equipment once doesn't their repair skill determine the amount the weapon is repaired and thus the cost of the repair? If thats true find a vendor with a lower repair skill its still going to cost you pricey weapons were designed to keep low level characters away.

Stash it someplace for when you get another broken sniper rifle. A broken weapon and repair another of the same type by 20% CND @ repair skill 100.

I think its fair the repairmen have a set value gives a reason to vist the cheap ones. And repairing a broken weapon should be costly for those who decided Jury Rigging wasn't useful.
You could also find a worse repairman. I believe Samuel Kerr at 188 Trading Post has a fairly low repair skill the second lowest after Dale Barton(The Fort).