Output driver settings for I/O pins

I think increasing current driver strength would indeed increase your problems since it is supposed to generate faster edges, then more emi.

The solution is a better and emi aware pcb design, possibly inserting series termination resistances on long traces. But I guess you can't change anything in your actual pcb.

Then you must somehow filter out the generated noise, but the optimal solution depends from several factors, i.e. operating frequency and type of signals involved.