Two ways are coming to my mind. The first one is using a software reset so you don't have to push the reset button manually. You should use this command to reboot your board:
The second way is killing the process and then restart it as you mentioned. To kill the process, you must know the PID of the process so you could use the following command:
ps | grep /sketch/sketch.elf
Then, with the known PID you can use the following command to kill it:
kill -9 [PID]
Let me know if this information is helpful for you.