There is no way to create an alias after you have deployed your system definition. Since you are providing your own custom LV interface, one option you might consider is to have your own built-in notion of aliases. For instance, you can create your own look-up with whatever names you like and then resolve these items to actual system definition paths or aliases. Since you own this look-up table, you can control it however you like, including adding or removing elements after deployment.
Just a thought...
Jarrod S.
National Instruments