Maybe you can lower the timeout, but 90 minutes should already be not the default (should be 24 hours), see:
http://forum.mikrotik.com/t/close-tcp-connection-after-specified-connection-time/17131/1
or (more complex, and only if the dst addresses remain the same):
http://forum.mikrotik.com/t/firewall-rule-how-to-drop-tcp-connection-lasting-more-than-3-hours/119215/1