Based on your circuit i cant see any obvious reason for the excess voltage. (Assuming your regulator is ok)
However, here's a few notes/questions that may help us narrow down where the problem is.
1) Connect AVCC to VCC, this shouldn't be the problem but your supposed to connect it.
2) Disconnect "Temp in" and "PWM out" from other things until you get the mcu working and 5V showing on VCC.
3) Did you get excess voltage with a new ATMega containing no code?
Yes = proves the problem is not to do with the mcu switching the fet and causing some sort of inductive spikes
No = Remove the fet and confirm 5V is present and the mcu is working (flash an led or something)
4) Check if you're getting this overvoltage issue with the ISP cable unplugged.
I very much doubt this is the issue but some programmers support 12V high voltage programming. It shouldn't be doing that but might pay to check its not trying to feed in 12V.
5) Do you by and chance have a large length of wire connected to this circuit? like 5+ meters
(eg, you might be building something that runs over a length of cable.) Any time you have a long length of wire and something that switching you can produce nasty higher voltages. I was once switching 24V through a fet from a micro and driving the signal into a 100 foot length of cat5. I was getting 160V ringing on the cable!
5) Can we have a photo of your circuit to check. (in case there's something wired up in a different way to your diagram /pcb and you haven't noticed it)
6) Put a 10k pulldown on the gate of that fet.
7) Double check that the VCC feed to your 2.8k and 10k resistors is actually from the 5V side of the reg and not the input side.
8 ) The copper tracks on your pcb, is that on the top or bottom of the pcb. I'm just wondering if there is a mirroring problem and the reg is connected up inverted.
(eg, reg pads are numbered for chip placement on bottom of pcb but the pads are on the top layer, or vise versa)