Let's not forget that the companies producing the genealogy software are in it to make money and hence their database formats tend to be proprietary. The GEDCOM import/export is an add-on to give us the illusion that it doesn't matter which software we use as we can always transfer our data via GEDCOM. This is simply not true. However, this does not address your problem. Your mention of SQL made me think of Rootsmagic which has a wiki regarding accessing Rootsmagic data via SQL
http://sqlitetoolsforrootsmagic.wikispaces.com/How+to+Query+...Rootsmagic can directly import a Legacy database without the need to go via GEDCOM. I confess I do not know if it is necessary to purchase the full Rootsmagic to do this or whether it can be done by Rootsmagic essentials but it is a route which might be worth exploring.
David