You don't need to do this. If the powers that be wanted to fake a referendum result, there would be much easier ways than manually rubbing out and changing pencil votes. (This would also be very difficult to do in the tight turnaround on UK counts.)
Countries that do routinely rig their ballots tend to find simpler ways to do it: Ballot boxes pre-stuffed with fake papers are a common trick, as is "losing" boxes full of votes from opposition areas. Rubbing out millions of votes is too much like hard work.
However, polls suggest millions of people believe the referendum will be fixed. Research by YouGov shows 46% of Leave supporters believe "it is likely the EU referendum will be rigged" and 28% believe MI5 is working with the government to prevent Brexit.
Still, if you really feel you must take a pen to the voting booth, feel free – it is allowed under the rules.