OH BBMom- Good question. I think that this issue could be an interesting one to look at, but wouldn't necessarily occur with only Heidelberg and Marietta. In the SCAC, Millsaps and Trinity are consistent regional qualifiers, and Birmingham Southern will be as soon as their probationary period is uplifted. In the NESCAC you have Trinity and Tufts. The LEC has Eastern Connecticut, Keene State and Southern Maine...and UMass-Boston surprised everyone last year by not only coming out of the conference unscathed but winning the New England region as well and advancing to Appleton. SCIAC has Cal Lutheran, Pomona-Pitzer and potentially Chapman, who applied for conference membership this offseason. The list goes on and on in other conferences (I'm sure some Virginians will get heated at the lack of mention of Shenandoah and Christopher Newport, same with Wisconsin and Stevens Point/Whitewater).
As infielddad mentioned, I think a lot of the regional placement has to do with monetary limitations at each school. My school was one of three from our conference to get into the regional tournament last year, and we were all placed in the same regional (2 Pool C's and an auto bid from the conference tournament). Ideally, of course, the NCAA should distribute schools according to their rank and match up (similar to how Division I March Madness is done) and not focus on the geographic parameters of the schools involved. But, of course, because we play Division III ball and lack funding, that is nearly impossible. And for the record, I'm pretty critical of the NCAA usually, but I really don't believe this is their fault.
I think the importance of in-region scenarios is extremely evident with the fact that teams that you play within 200 miles of your campus are weighed into your overall "region record" by the selection committee. At least they're doing something...right, wrong or indifferent...to try to make the situation more justifiable.
If schools like Marietta and Heidelberg get split up, they could very easily end up in the CWS together like you said. And if they don't...it'll be one hell of a regional.