Access Gateway Standard (Model 2000) version 4.6 is out for some time but it looks like Citrix forget to mention an important feature! I outlined the functionality to Citrix during the beta test of 4.6 and even said they should document it. I couldn't find it in the documentation and even the online documentation of XenApp 5.0 FP2 states that it would require the Advanced Edition.

With 4.6.x you are now able to partly use the "Access control" feature of XenApp published applications. This allows disabling applications in Web Interface when coming through the Gateway. This is NOT just hiding the application is disabled in that scenario.

Be aware, by setting the Access control option you break session sharing on purpose for the application otherwise the app would be reconnected when connecting through the Gateway. The filter option are only working with the advanced edition.