This line really does make one wonder such a scenario. So it's a general consensus for all of us that the higher tier espers like level 5 were very recently. All of us here can agree on this point, no?
I wouldn't put it past Aleister if he's secretly developing anti-esper weaponry that could potentially nullify their abilities based on observing Touma's Imagine breaker or another method that cancels AIM based powers. It's already confirmed that Full-Tuning and other Misaka WORST are yet to be unveiled.
I can understand if Accelerator was the very first lever 5 discovered since many of Academy City's esper ability enhancement projects use him as the base like the Dark May Project.
Although Academy City is self-sufficient in many areas, it still needs to bring in raw materials from the outside.