Capacitor on mosi/miso lines
If the 4.7nF between two of the ISP pins, you may well have issues unless you slow the ISP clock rate down quite considerably (&lt;1MHz) otherwise the signal edges will be slowed possibly to the point of not being recognised.

You have two options that I can think of:


Use some 2.54mm header jumpers that are placed between the MCU pins and the touch sensor components (caps, resistors, etc.). When you want to do ISP, remove the jumpers so that the ISP pins are now isolated from the rest of the circuitry, leaving only the ISP header connected. Once programmed replace the jumpers.
Use solder jumpers to isolate the circuitry. Do a one-time programming of a bootloader, then solder the jumpers. This way if you need to reprogram you can use the serial port rather than the ISP pins to do so. In the event that the bootloader gets corrupted, you can desolder the jumpers to use the ISP again. 


The advantages of having a small solder jumper vs a 2.54mm jumper header are firstly the space used is much less, and secondly the impact on your touch signals from parasitics of the jumpers is minimised.