What exactly is the difference between using this and the freebase api? Are they just converting data formats?
In SPARQL you can write queries that involve any graph relationships that come into your head. You can take the UNION of multiple graph patterns. With SPARQL you can also get back 200,000 or more results.
With MQL you quickly run into the wall when you find that you can't write the query you want (you need to write 10,000 queries instead of one) or that the query you want to run times out, or that it only lets you get back a limited number of answers.
It's also possible to do batch processing with :BaseKB Pro with extreme efficiency. We did a calculation that would have taken 100 years on the biggest machine in the AMZN cloud in SPARQL in just 24 hours on a mac book pro with an optimized pipeline.
More likely, you'll need to rebuild the dump to be more than quads ordered by arbitrarily assigned unique id, and with nearly 600 million quads, it's not completely trivial to do, might involve temporary index files, etc.
Still, it's doable.
(also see: http://code.google.com/p/freebase-quad-rdfize/ )
SPARQL is harder to learn and set up, but allows for more complicated queries that might require offline processing.
(I designed the first version of MQL)