NO TO PUNISHMENT!
Punishing players for showing skill is a bad idea for all the reasons people have stated above. If there is a problem with newer players having very little chance, then it makes more sense to tweak some of the default settings - in other words make changes that are the same for ALL players. A level playing field.
You could rot health and armour over 100 proportional to the square of the excess for instance (so if you have 300 its going to rot VERY fast!), or reduce the "rot delay" time for large values of health/armour.
You could reduce the power of various weapons.
Players could spawn with 50 armour instead of zero.
Reduce hitbox sizes or introduce "headshot" code to make Nex-sprees harder.
Spawn protection to prevent the more skilled players spawn killing.
You could probably add more to the list - the point is that the game can be made more "newbie-friendly" WITHOUT "punishing" better players, if the will to do so is there.
On the idea of new-player servers: I was an admin for three years on a UT99 new player server. The only way to make that work, and prevent ****ers using it as a warmup server or just being unpleasant was to have a team of nearly 20 with kick and/or ban powers dedicated to keeping it clean. We would personally kick something of the order of 1000 times per week, and I had to clean the banlist weekly (around 100 bans per week). In addition we had automated systems that would remove another 2-3000 players per week. Running a new player server is hard.
I have popped in to the "new players" server that DCC run to try and give help and advice to new players - all credit to DCC as well, but unfortunately there are enough skilled and semi-skilled players owning there to frustrate the genuine new players. New-player-server-specific-settings are of limited use as well - if the settings are too far away from "regular" settings, then the new players end up learning the wrong game. Instagib could be useful for new players, allowing them to concentrate on just movement, position and aim, but for the fact that in Nexuiz it is very easy to hit other players, and so skilled players own there as well.
In short if the community wants to make things easier for newer players then tweaking some of the settings is much fairer than punishing skilled players, which in my view is a bad idea. The community doesn't
have to make it easier for newer players though, but I would comment that I have introduced the game to 6 or 7 experienced UT players, all but one of who gave up because they felt as though they were just cannon fodder.
Personally I actually like the game just the way it is, but it would be nice to encourage more to play it.