Well it sounds like you aren't going to touch it, but if you think about it from a lore standpoint Conjuration bypassing MR doesn't make complete sense. While Conjuration is distinct from Evocation in that; rather than bringing forth forces or items of pure magic or elements, Conjuration calls up a real item or creature either from another plane, place or possibly from a conception in the caster's mind (presumably a conjurer could call up one of Plato's ideal perfect triangles). Nevertheless that item or creature owes its existence or connection to the current plane to an act of magic, you might say it is tethered or bound by magic. Thus a dismissal spell will banish summons and extra-planar creatures, even though they are "real". So presumably if an insect plague spell hit someone with high magic resistance and they passed their percentage check the insects would simply disappear in little puffs of smoke as the magic guiding and keeping them there is gone (same reason these spells have durations). Having never played much 3rd Ed. I can't speak for how it worked then or how the rationale went, but the merit of this argument is that it doesn't require any extra work!
Also regarding adherence to PnP, I'd say the greatest merit there is acheiving some kind of consistency, in the original game and between mods. I'm biased in favor of 2nd Ed. PnP but as you say there are some things that just don't make sense, or at least don't work well in a CRPG context (the 2nd Ed. Stat system for instance).
Just my two cents. Demi, no pressure or nothing, but I sincerely hope you don't get burnt out on modding in the near future. I'm looking forward to the day I can play a near perfect BG experience with IR,SR,KR (QR, CR?) and SCS.