1.06 will be fixing the unarmed damage bonus applying to thrown attacks and crossbow attacks. The problem I see here is that unarmed really doesn't keep up on the lower levels. Starting at about level 7 you aren't going to want to melee much with unarmed anymore. The damage ends up pretty low. Unarmed+Crossbow/Unarmed+Thrown were the only good use of unarmed I found. It seems like when you take this away it is going to really, really hurt the skill line. Perhaps it needs to be buffed to compensate. Something that grows with level to help unarmed keep up near the bottom. Archery and Thrown without the bonuses from unarmed also seem a little lacking.
Unarmed does get the benefit of being able to go dual-shields. As a consequence it should be less good in other areas than the melee builds that actually use, y'know, weapons. Though it is true that the converse skill, dual-wielding, gets some very useful defensive stats (mostly counter chance, but that is after all the best defensive stat) and still gets the benefits of using two weapons at the same time. So one or the other is probably on the wrong end of the balance curve. I will say that archery and throwing are not especially great skills as it stands. I suspect this is largely due to procs not working on ranged attacks, which makes it hard to code buffs or active skills around them.
You can go pure unarmed no problem, I did at least. You'll get up to 30 damage or so and you can get higher. 1) Take assasination or berserker or both. 2) you can take tinkering for overclockworked limbs for an extra 10 damage. 3) If you put your points into mostly warrior skills you'll end up with about 15 or so melee power. You'll end up with about 40 or so damage given a few damage enchants along the way with about 50% crit rate and 100% block. Additionally you'll have like 35+ armor with a shield/master of arms/shield bearer build. I think my build was unarmed/shield bearer/master of arms/vampirism/fungal/assasination/smithing. But I could see taking tinkering instead of smithing. But a full plate massive block unarmed build is pretty viable. DL 7/9 can be a tiny bit tough. But 8 is a breeze. And DL 10 isn't too bad.
I was able to beat the game on the middle difficulty level without very much difficulty. I even kicked Lord Dredmor to death without using a single bolt or spell, just my feet of fury. Dual shields, unarmed, assassination, psionics (for radiant aura) and master of arms (for suit up) were how I did it. I rarely used any magic and kicked just about everyone to death. I feel there is a lot of power to an unarmed character, at least with those skills. I also had perception for trap detection and second sight (awesome!) and then promethean magic, which I only used in the rare instances where I was overwhelmed. It didn't feel true to my character though, so I kept that minimal. I never had problems with damage. Radiant aura really, really helps with that and it would stun everyone around me, which kept me much safer. Most of the times when I'd die would be my own fault due to stupid mistakes. Even arch diggles were only two hits sometimes, so the only challenging part of the last floor was when I finally ran into Dredmor himself. Unarmed is a kick-ass skill to use. I'm also learning to really like fungal arts on a new character. It comes in really, really handy. I never would have guessed I could clear out a monster zoo just with those puffballs, but they are powerful!