Now that you've speculated, I thought I would check some facts. I don't have any programming skills so I can't do any sort of thorough analysis, but I decided to do a quick look over the profiles of Feliks Zemdegs and Rowe Hessler, and Michal Pleskowicz, the top three cubers in 3x3 speedsolve at the 2011 World Championships, and also acknowledged as among the best cubers in the world. There weren't a lot of examples to go by, but I will post some of their averages that included DNFs to see how destroyed they were. Except they weren't destroyed at all:
Feliks Zemdegs:
3x3: 7.78, DNF, 11.27, 6.77, 7.58
Average: 8.88. WR single, 6.77
NOTE: The DNF was the second solve in the average.
Not only did he get what was a reasonable average for him, certainly not considerably better or worse than anything else he was getting (at the same competition his other averages were 9.07, and 7.91, which became the WR average), but two solves later he went and got the new WR single! This, of course, happened just after he had beaten Erik's long-standing 7.08 WR earlier in the competition.
4x4: 38.28, 40.91, DNF, 36.84, 37.00
Average: 38.73
In this case the DNF came in the middle of the average, and after that he proceeded to get the best two times of the average. The average was not the best because of the solves that came before the DNF, not after.
2x2: 3.31, 2.80, DNF, 1.61, 2.93
Average: 3.01
A normal average for him at the time (which, incidentally, was followed in the final round by the OcR), Feliks once again proceeded to get his best solve after the DNF.
Megaminx: 1:02.86, DNF, 1:05.47, 1:09.80, 1:02.58
Average: 1:06.04
Even though megaminx isn't one of his main events, I thought I'd put this one in there too for the sake of it. This is the current OcR.
Also from Feliks, the old OcR in Square-1 had a DNF on the second solve. The current OcR for OH has a DNF on the final solve (this doesn't show much re. the meta thing, but still shows that a DNF is not necessarily devastating).
Rowe Hessler:
3x3: DNF, 9.96, 9.44, 10.40, 9.56
Average: 9.97
A brilliant example of why all this "meta" talk is a load of crap. Rowe's most recent attempt, a DNF on the first solve, followed by a decent sub10 average.
3x3: 11.13, 8.88, DNF, 9.44, 8.38
Average: 9.82
Just another example of a fairly recent average. This could have been significantly better if not for the 11.13 on the first solve, which is unfortunate. I'd be interested to know if that was a +2 or not.
4x4: 41.66, 39.91, DNF, 44.59, 36.40
Average: 42.05
Rowe's PB 4x4 average in competition, the best solve comes after the DNF, once again.
2x2: I won't pick out any specific cases, but if you look through all his averages there are a few with DNFs in them and they are mostly normal averages, and certainly no exceptional cases of a DNF completely destroying an average except one occurrence of two DNFs. But this only shows to me that he obviously didn't care enough to be careful after the first DNF (which is what you meta-argument defending people seem to think would happen, that is, people would slow down a lot and be more careful after an early DNF).
OH: 13.03, DNF, 13.86, 18.19, 16.05
Average: 16.03
Just one of a few examples from Rowe's OH averages. This is once again a normal average for him in comparison to other competition averages. The DNF is followed by a very fast 13.86.
Michal Pleskowicz:
Our current World Champion is a good example of how you can avoid DNFs if you put your mind to it. He has a very good record regarding these. Unfortunately there is no information on his +2 penalty history for misaligned slices. I'll just point out a couple of averages that show that DNFs do not destroy averages.
3x3: 10.21, 8.33, 9.93, 9.68, DNF
Average: 9.94
And an old average of his from 2009, which was his PB at the time:
3x3: DNF, 15.09, 14.38, 17.27, 14.90
Average: 15.75
Because all of this was such a successful endeavour I thought I would have a quick check of the averages of two previous World Champions and also highly respected cubers.
Breandan Vallance:
3x3: DNF, 9.28, 10.13, 9.21, 9.27
Average: 9.56
A recent average for him, and the best he had done in quite a few months.
3x3: 9.00, DNF, 8.88, 9.46, 10.77
Average: 9.74
Done at WCs
3x3: 9.33, DNF, 9.21, 9.78, 10.63
Average: 9.91
The winning average at USNats 2011.
Yu Nakajima:
Another example of how you can solve the cube when you put your mind to it, not a single 3x3 DNF!
4x4: DNF, 1:08.68, 48.44, 48.41, 46.06
Average: 55.18
This is the only case I have seen of a DNF "destroying" an average, except my guess is that it was actually a big old POP that destroyed the average, and not his meta, seeing as he proceeded to get what were good times for him after that.
5x5: DNF, 1:23.09, 1:29.05, 1:19.11, 1:16.41
Average: 1:23.75
The NR at the time.
So what can we conclude from all this? Firstly it should be made clear that we cannot conclude that changing a +2 to a DNF will have no affect on cubers. All of this had no information on +2, nor on how changing the rule would affect the meta of elite cubers. However what it does show is that elite cubers are not concerned in the least by getting a DNF. Therefore I think we have good reason to believe that the meta of cubers would not change significantly in the face of a change of rule, as penalties in general are a rare occurrence (thanks to the data provided by keyan), and even when a penalty is incurred the elite cubers simply don't let it affect them.