I'd go with FileBooks, despite the licensing.
Even if there were 3 or 4 competing FMP accounting packages, your CPA would likely have never used any of them (neither would your auditors,
their auditors, etc.). We generally recommend custom software for places where you don't want to "do it the way everyone else does", where you want to put your own stamp on your business and its workflow, to pass your insights down to the next generation of the company. Accounting, however, is generally one of the areas where you
want to do it the way everyone else does: or at least the way your CPA does.
If things like FileBooks, let you remove redundancy while letting you use a standard accounting package, that seems like a good deal. (Similarly, if ODBC lets you remove redundancy while using some other accounting package, that would seem good as well).
By the way, QuickBooks isn't the only commercial accounting package to integrate tightly with FMP.
MoneyWorks isn't that well known in the states but is big in NZ. They have had built in FMP integration for years and have been coming to DevCon recently to show it off. They'll even supply copies for your accounting firm if they're not already using it.