Sure a 30/40 seater (forgot that Aurigny have dumped the Saab 340, so it would be down to an ATR42) is more expensive, but I do not think that GCI and JER exactly need a 0.00 GBP*-fare type operation to CDG that flyBE offers (and needs to have subsidized with a rather hefty sum obviously). Why are the islands after a low cost operation for a route that, me thinks, is more important for the business clientele that needs access to an international hub ? Charge more realistic fares that require less funding - and also save business travellers from having to pay for putting stuff in the hold, checking in at all (soon to come), having a cup of tea etc.
FlyBE wanted 1.6m GBP for the route. Over here in Germany, you get a twice-daily route with a 34/36seater for a subsidy in the range of 500.000 GBP - 900.000 GBP, depending on the conditions of the contract (numbers quoted are for the routes KEL-MUC and RLG-MUC which are much longer than JER-CDG). The islands should put out the route to tender.