PICKIT 3 resets PIC16 three times upon reprogramming
You can't.  The programmer is probably resetting the PIC as part of the programming process.  For some PIC 16 MCLR must be held low and then raised to Vpp to enter programming mode.  On some newer ones the MCLR voltage can stay within the Vss to Vdd range, but the chip must still be reset by driving MCLR low.

What's the problem anyway?  You can't be expecting normal operation during programming, so what does it matter if MCLR is asserted?