He'd also have to completely remove the Antimatter Relays as well, and restrict the types of transmutations. What really broke EE3 wasn't necessarily the collector arrays, those at least required resources to get going (albeit at a geometric rate as your first array provides the materials to make the next, and so forth). It was the mooshroom farms and darkrooms which produced boatloads of free EMC. And you could get that going as soon as you got your philosopher's stone (transmute any passive mob into a mooshroom) and your Antimatter Relay (to turn bowls of mushroom soup into EMC).
Energy Condensers were another big culprit, basically an automated trans tablet that made whatever you wanted made when you give it stuff. I remember lava cells were the same EMC value as coal, which made keeping geothermal generators topped off pathetically easy (not that it isn't already easy, mind you). But IIRC, the Condensers were a big part in getting the collector arrays going to produce EMC in a solid form to store.
Remove the Collectors, AMR's, and Condensers and you'll have a much more balanced mod.
The only recipes currently in EE3 that might be exploitable is the Iron -> Enderpearl recipe and -maybe- the obsidian ones. But even there, it runs down endurance on your proto-philosopher's-stone, which is non-trivial to obtain.