You can, but I think you are probably not looking at the best solution. This link has details of how to program the "OS" timer http://www.switchdoc.com/2015/10/iot-esp8266-timer-tutorial-arduino-ide/ I haven't tried it, I'm not even sure it will work, but...
The fact that setting the timer interval to 2uS causes issues with the WIFI implies that it might not be accurate enough for your purposes. It might be better to use "something" to trigger a HW interrupt. From the moment the interrupt triggers to the moment the signal is sent out on the pin is a calculable finite time, so rather than 2,000,000 uS you want the event to trigger after 1,999,524uS (that's a made up number).
Of course if you are using a device that can trigger a pin on the ESP8266 there is no reason it can't trigger the 'output' pin, without involving the ESP at all.
You could use an RTC DS3221(?), the ESP sets the time on the RTC and then sets the alarm. The alarm interrupt pin is connected to the ESP and it relays the signal to the output, or the alarm interrupt pin is directly connected to the output pin. The limiting factor here is the accuracy you require.