This is with the Rodeostat correct? Going over 100uA shouldn't be an issue. There are four current ragnes +/- 1, 10, 100 and 1000 uA. So ideally you would use the 1000uA current range setting? But even in the +/-1, 10, and 100uA ranges going over 100uA should not cause any damage to the potentiostat or the computer. Your current measure will clip at the limits of the range, but otherwise it should be fine . If you think it might have more than a couple of mA then you might want to take measures to limit the current.
Yes you could definitely use the Rodeostat's teensy 3.2 to control the LEDs. On the Rodeostat PCB there are two 5x2 expansion headers which expose various DIO pins on the teensy which you can use. The ability to toggle the expansion header IO pins via USB commands from the host PC is not included in the standard firmware . So you would need modify the firmware to toggle these pins - to control the LEDs - yourself.
The firmware for the Rodeostat is just an Arduino sketch. so if you are comfortable programming Arduinos modifying it should be pretty straight forward. You could probably quickly hack in this feature by adding a few lines to the SystemState's "updateTestOnTimer" method - just check the time and set desired digital outputs for the LEDs using digitalWrite based on time or the current measurement, etc. The "updateTestOnTimer" method can be found in firmware/libraries/potentiostat/ps_system_state.cpp starting on line 353. With the default settings it is called at 5kHz - so every 200us.