Unless you are using an oscillator with a sinewave output, the EMI contribution of the connection between it and the XTAL1 pin will be far greater than anything the XTAL2 output might produce. That would be my main concern!

I do agree. Just disconnect anything unneeded from 'XTAL2' pin, and do this very close to this pin, means avoid any copper trace connected to it.

Oleg, if you really need extreme low radiation levels, then only a four layer board should be used!! Even when using double sided PCB containing solid ground plane, you will result in much higher radiation levels as with multilayer board. Using a shield enclosure is highly recommended. But choosing proper grounding point on PCB can be troublesome...

Does any cable leave your board? If so, then you can totally forget radiation of 'XTAL2' pin, because then cables will heavily emit even the least amount of ground noise (common mode noise). In such a case, enclosure must be grounded to PCB at the same point, where the cables leave the board, means, where the cable shields are connected to enclosure.

You will very probably need some common mode filtering, means the use of soft ferrite common mode chokes directly at cable entries. I would use the following concept:
Provide separate PCB area directly at cable entries, which does have a very proper connection of local ground plane to enclosure. This connection point is the location where the cable shields have to be connected to. Don't share this local ground plane with ground plane of microcontroller circuit. Connect from each signal line a transzorb to this local ground plane, which is sometimes called 'chassis plane'. Keep in mind, that signal ground must be treated in the same way as any other signal! You can parallel capacitors, if bandwidth of used signals allow this. So, this already gives you a very effective protection egainst ESD, without violating ground routing of microcontroller board. Directly at these transzorbs/capacitors connect the signals to a common mode choke, where the one side sits on chassis plane, and the other side sits on ground plane of microcontroller board. Place the choke over a gap in ground plane. Connect on microcontroller's board side also capacitors from each signal to ground, but not to chassis ground, of course, but to microcontroller's board ground. This gives you a very effective PI-filter.
Make no mistake, ground plane of microcontroller board must also be connected to chassis plane, but in such a way, that currents through transzorbs/capacitors will not erode ground potential of microcontroller section. Means, everything connected to chassis plane must see a perfect, low ohmic and low inductive connection directly to chassis at this point. Not by only one screw...
If more than only one cable have to be connected to your board, then this should be done at only ONE point. Otherwise common mode noise resulting from interference running across the whole board becomes so high, that even extensive use of filtering will not help any longer.

By the way, Michael Karas has published a very nice scheme using common mode filtering a while ago. But I don't remember where. May be he can help us?

Kai