The Intelligent Message Filter did not provide a mechanism to skip filtering for specific recipients so far. This changed with a new hotfix released recently. The update is available through Microsoft Product Support Services and is planned for release with the next Exchange service pack.
The update requires creating some registry values. Here you would identify the list of recipients to be excluded from filtering. IMF would then verify incoming email recipients against this list and skip processing accordingly.
This functionality brings more flexibility when configuring IMF. Consider a setup where IMF gateway blocking is set to Archive/Delete/Reject emails. Some mailboxes may be considered to be too sensitive to risk a false positive. It is true that the IMFv2 false positive rate is very low and compares well to other commercial solutions. Nevertheless some organizations prefer it this way, and the new hotfix addresses this requirement.
A step-by-step description of the registry configuration is available from KB912587 - Exchange Server 2003 Intelligent Message Filter does not provide the functionality to exclude a particular recipient from anti-spam filtering.