Ouch. This would be very awkward to handle.
Yes, currently very little of the metadata in a Tile Entity is modified by rotation.
In v2.7, the rotation of Mobs (including minecarts and armour stands) is preserved and rotated, as is any entity with a 'Pos' and 'Rotation' attribute.
There is also a new provision (initially made for Carpenters Blocks addin) that allows you to (in the config file) specify a tile entity type, and a corresponding attribute and its rotation states. This is intended to handle custom blocks that hold their rotation in their tile entity. A separate rule allows you to define rotation states for custom blocks that hold their rotation state in their DV as with normal blocks.
The problem here is that command blocks have just a large text Command attribute, which would need to be parsed, any relative coordinates identified and modified and then a new command string generated. This would not be a simple procedure. This is made even more complex by rotations -- so "~3 0 ~" would rotate a quarter-turn to become "~ 0 ~-3" and it would be even more complex if you had something like "~2 0 0", not to mention for commands with multiple coordinate sets.
Commands to be affected would include blockdata, execute, fill, clone, particle, setitem, setblock, spawn, spawnpoint, stats, summon, testforblock, testforblocks, tp; I can see how many of these would be in common usage in many adventure structures and would need to rotate properly 
I can see a way to eventually achieve it, but I hate writing string parsing in Java - I've been spolit by the easy functions in Perl...
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tmp.cfg [5.52 KiB]