Basically you can use the Profile feature that comes with Spring 3.1
In the nutshell what would happen is you'd have two adapters configured under different profiles:
So as you can see I have two adapters configured under different profiles. However only one adapter will be available depending on which profile is active.
<beans. . . .>
<int-file:inbound-channel-adapter . . ./>
<int-jms:inbound-channel-adapter . . ./>
. . .