There's no perfect solution to this really. Obviously if they're found guilty on a wider scale then Wrexham etc... could claim they've also been robbed, and they have. Similarly I'm sure there's some relegated sides who could claim that Southampton took points off them which may have caused them to be relegated etc.... Or Arsenal may say it's cost them a chance at a treble. You could go on for ages.
But, really, Boro are the ones who it is immediately impacting, in a direct game against them which impacts *directly* promotion. The rest is all indirect and permutations.
I'd say that for the Boro match they sohuld be given a 3-0 win for the first leg, and then the FL investigate the wider offences (Ipswich, Coventry, Wrexham etc....) and go from there in terms of fines/points deductions.
If it's a sustained cheating operation, then they should have points deductions coming into play next season too. Fines won't put anyone off.