When MMA refers to small joint manipulation I believe they are talking about fingers and toes and such - wristlocks are not prohibited to the best of my knowledge. (With reference to Loudenvier's comment) Also, Loudenvier - though some of Gozo Shioda's demonstrations appear absurd, he is the founder of Yoshinkan Aikido, and demonstrations aside that style has a reputation for being the 'hardest' Aikido style with some of the most effective training. Also, as CK-sensei mentioned to you in another thread, Gozo Shioda took part in a match against one of Kimura's deshi, in which he broke both of the student's arms. However, this is all by reputation, I have no personal experience with Yoshinkan.
One thing that should be considered is the possibility that Aikido has long since been taken well out of context. Most, if not all of the earlier important figures in Aikido were also dan ranks in Judo, many of them high ranking. Also, in his book "Total Aikido" (and elsewhere), Gozo Shioda quotes Morihei Ueshiba (the founder of Aikido) as saying "Aikido is 70% atemi" or something to that effect. This can easily be assumed to mean that, contrary to what modern training practices might indicate, no one is expected to be able to simply grab a punch or a knife thrust mid-flight and use its momentum for a technique. Instead, in a real fight, kuzushi must often be generated by striking, much in the way grappling techniques are often set up with strikes in modern MMA.
I am not an expert, and do not consider myself at all knowledgeable, but it seems to me as if the functional range for most of Aikido's techniques seems to be a sort of mid-range area between closer than that of striking yet further than that of the clinch, in which you would apply Judo knowledge. It also seems that one of the functions of Aikido's tai sabaki is to maintain this range. Against a single opponent, a confident Judoka may wish to clinch where they might dominate an opponent, or a confident striker might stay at range where they could pick apart an opponent with their best skillset. On the other hand, against multiple opponents it seems you would not be able to stay at striking range for any amount of time, nor would you be able to clinch for any amount of time for fear of being tied up and pummeled by the other attackers. In this situation perhaps you might want to use tai sabaki to flow through this mid-range applying atemi or techniques as you saw opportunities, while looking for a means to escape if that was an option.
It's interesting - Tomiki aka Shodokan Aikido actually has their own form of randori and shiai (its founder, Kenji Tomiki was 8th dan in Judo incidentally). There is one type of randori/shiai where the two opponents try to throw/lock eachother in tachiwaza, and another more interesting type where one competitor has a rubber knife, and tries to stab the other, while the other tries to throw/lock him. It is certainly interesting, but seems very awkward because the competitors are limited to using the 17 randori techniques of Tomiki Aikido. While they all seem to be potentially very effective techniques, it seems like very often Judo techniques would be MUCH more expedient in the one-on-one clinch situations these competitors find themselves. Here is a highlight video from a Tomiki Aikido Shiai:
http://www.youtube.com/watch?v=XwkvpLtmTHo...feature=related - more can easily be found by hunting youtube. Also, if you are curious,
http://homepage2.nifty.com/shodokan/en/ the Tomiki website has plenty of interesting information, including the aforementioned randori techniques.
In closing I'd like to say that I am in no way qualified to pose any of the above as a serious argument. It is purely conjecture, though I hope it is at least somewhat interesting