Just wanted everybody to know, that in the upcoming Beta1 of BizTalk 2006 it will be at last possible to remove MSMQT adapter just like any other. You still will have the code on the machine (it's actually part of the core engine and cannot be separated), but you will not see it in confgiuration, it will not lock the port 1801, and you can run MSMQ (a.k.a. MSMQ/C) adapter without configuring it side by side.
You still should be careful doing so. If you remove MSMQT adapter with some messages still waiting for the delivery, and later change your mind, you must remove those messages manually before you decide to add the adapter back.