First of all, great OP. A little complicated for my taste, but something of the sort needs to be implemented.
Now my Thoughts:
During the day in my kin(a primary raiding based kin, with a few casual players thrown in.) we usually run 6-mans. Sometimes we'll just throw the 3 GB's and OE and Glinghant, these are all short, usually sub 20min, mostly sub 10 if we have a warden who can pull half the instance at a time. These instances give us a fair amount seals depending on the run, 4 for sammy all the way up to ~10 with Glinghant. After a few runs we will usually throw some others in there, an HV, a bells, or an SG, a Fornost. These instances are all longer and more difficult to run, but most give more seals, ie around 10. However for us these are still somewhat of a face-roll, so we feel little to no challenge. Sometimes at night when we don't have enough for a raid we try the harder 6-mans, ie Sari-Suma, LT, Shadow. These are more difficult and actually give us a challenge, they may have not as many seals, or not give us any gear that we want, but there fun so we try them anyway.
We the above in mind, here is my addition to your suggestion. Lets say in addition to the time factor they adjust it by difficulty, so even if there are some shorter runs that are still fairly difficult, ie Fornost, or Bells for example. These still would give more seals then say a similarly long run that is easier, ie sambrog or thadur) in addition, group size should also be taken as a factor: Disease Wing in OD(T2C) gives 4(?) seals, when Glinghant gives 10. IMO the more people in the group the more seals that should be given. Even in the above example, the raid gets 48 seals total in Disease, when the fellowship gets 60 in Glinghant (totals). Even if it isn't higher seals per player, it definitely needs higher seals per group.
1. More seals based on difficulty(not just time-investment)
2. More Seals based on Group Size(4 for seals for a raid vs 10 seals in a 6-man? I think not!)