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you cant do the same as the minium stone as you don't right click to pickup the block, and bukkit plugins cannot detect a key press as far as my knowledge goes, i currently have the function disabled within the portal configs itself. the easiest way
I dont think its possible to block the pickup ability of the portal gun at all due to the nature of the way its coded, but you can disable that function in the portal gun world config inside your world folder.
take a look at this, patches the EE tools to not bypass at all without the use of a plugin.
http://www.planetminecraft.com/mod/tekkit-eepatch-recompile-312-tekkitrestrict-bug-fix/