Brandon Allen has put up decent stats in the minors, but he has some major deficiencies to work on before he hits the pros. First off, he is prone to striking out alot (124 in 2008 in 516 ABs) his fielding is sub-par for a 1st baseman (15 errors) and his average is, well, average for a minor league player (.279).
Whitesell is prone to the K as well, but he makes up for it with a higher average (.324) and OBP (.424). So aside from age, which really isn't a factor, I don't see how Allen is a better option. Your argument is based on the lack of experience he has in the majors and irrelevant D-Backs history. Remember Upton? He tore up the minors so fast that the organization couldn't wait to get him into Chase field, but he lagged for a bit but then caught fire. My argument is that we have nothing to lose by letting him finish out the season as the primary 1st baseman and seeing what we have in this kid. If he still sucks after 200 or so at bats, then I'll be more than happy to eat crow; however, at this point he is the best option we have and there is potential for this kid to stick around.