Can the Galaxy S2 be rooted without increasing the custom flash counter using adb?
You can make or buy a USB Jig for Samsung Galaxy S2 i9100. It’s a really simple circuit that involves putting 300K Ohms of resistors between pin 4 and 5 of the microUSB connector.

With a USB Jig you can reset the custom binary counter to zero and also remove the yellow triangle on start up if you have rooted your device. 


Turn off your phone completely and remove the battery for 10-15
seconds 
Put the battery back but don't switch on the device 
Plug the USB Jig into Micro USB port of your phone Wait for around 2-3 seconds
You phone screen will show "ERASING DOWNLOAD INFORMATION SUCCEEDED" in ODIN mode and Custom Binary Download : No
Now you can remove the battery and restart the phone.You will also notice that the yellow triangle which comes at start-up is gone now.