Free Companies has a morale mechanic in it as did the alternative mass combat rules which used to be up on the site but i dont think they still are. Both are intended for large scale battles in mind really. i know you are running Kovag Re for your intro adventure and with such small forces used i would go on gut instinct for a ruling on morale. look at the average will save, whether they are highly trained soldiers, fanatics or just filled with good old bloodlust? then look at their equipment is it good, average or of low quality? compare that with how many of their comrades have bitten the dust and go from there.