I think requiring fleet supply is the wrong approach....I'd much rather make it more difficult to get an SB to a gravity well (ex: it must be friendly, it must have phase node, the SB gets debuffs after exiting phase space, etc) or require individual SBs to make sacrifices other than fleet supply in order to jump (ex: they require 1 or more special SB upgrades in order to phase jump)...
I'm in agreement here and part of the reason is that I don't think fleet supply will be as much of a disadvantage as people are assuming. The problem is that for every other "ship", you can't start building it until you have available fleet supply. If you don't have fleet supply available, the ship waits in the queue until fleet supply becomes available. With an Orkie that requires fleet supply to jump (I'm assuming that it is an upgrade that allows it to jump), you can construct it on your front line and make it combat ready before you research its fleet supply. This is a big advantage.
So let's assume you are a VR in the econ spot. You want to push 4 Orkies - 1 each to support your teammates on your immediate right and left, 1 to push up the middle, and the 4th as a reserve. You build the colony ships, send them to the front lines and begin building each starbase. You complete each Orkie to 7 levels (assuming the 8th is the jump upgrade). This takes a considerable amount of time, time in which you still don't have fleet supply penalities. When you are ready to attack, you then bump up the fleet supply and upgrade the Orkie. You still get most of the economic benefit that you have now because you can delay the fleet upgrades while the Orkies build.
What makes this effective is that the building Orkies are playing a valuable role even before they are jump capable. They are helping to defend key choke points for your team. They are projecting military power and have the potential to attack later on.