Chris
Apologies for not realising ASA v8.x now has an ability to make an ACE inactive, good to know.
This one however i do know as i have faced the exact same problems with SQL. Prior to v7.x you could only set the timeout globally but now you can do it with the MPF (Modular Policy Framework) so you can use a class map to match specific traffic ie SQL in your case and then use a policy to set a connection timeout for that type of traffic. See the examples section in this link -
http://www.cisco.com/en/US/docs/security/asa/asa82/command/reference/p.html#wp1879322
Jon