Anyway our board is for device where even small EMI may cause problems.

Have somebody an idea about it? Does any capacitor/resistor on XTAL2 may decrease this EMI level or should we use hardware shield over the whole board? Or, as last case, maybe am I so paranoic to think about such EMI sources?

I do not know any way to 'kill' XTAL2 (output) since it probably is the internal source for the clock. If you are supersensitive to EMI use a chip such as SILabs F12x which has a PLL and you can run very fast internally with a low clock frequency (also, it being a one clocker helps).

Erik