If you are not using certain SERDES Quads, it is perfectly acceptable to use the pins in the keep out areas of the unused SERDES Quads for I/O. This is only if there will not be any traffic on the SERDES Quad.
These pins are listed in the hardware checklist. For ECP3, page 5 of the hardware checklist application note lists the aggressor pins.
http://www.latticesemi.com/documents/tn1189.pdf
There is a preference the user can put in the ispLEVER or Lattice Diamond constraint file that will force the tools to not use the I/O specified. The constraint takes precedence over any other locates and helps to ensure the aggressor pins are not used.
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