Unless you can specify what _exactly_ "the Instance should be flagged as completed" is supposed to do it's a pretty useless idea, sorry. Most instance-related deeds involve solving multiple specific tasks like challenge mode, and allowing to bypass those requirements would render those deeds worthless.
As for the slayer deeds: I think almost all of those are for fixed-level instances (Moria/Angmar) and should be soloable by a level-cap char with little problems (most of those instances could be soloed back at level 75 already). And most scaling instances shouldn't be a problem either as you can scale them down to their minimum level. Which leaves very few cases where your idea would actually apply.
Besides, the implementation of your idea would couse quite a lot of issues as "any associated Deeds (Kill 999 Orcs in <<Instance>>) should be changed to a non-Instanced alternative" means that any such deed would require a clone, and any other deed having it as a requirement would have to be able to accept both versions, which AFAIK isn't possible in the current system. As a software developer I can tell you such a change simply asks to be abused.
Btw, I understand your motivation given that I cleared all landscape (except HD and Moors), Angmar and Moria instance deeds on my main char. If those achievements could now be obtained by simply exceeding a timeout I'd not be pleased, and that has nothing to do with "huge elitist Raiding Kinships" as most of them are the result of extensive solo grind.
And I second the advice to just ignore the instance finder. There are several good reasons why it's not used at all for setting up groups. It's called _Instance_ Finder, not _Group_ Finder after all.
Used to play: 85 Champ / Captain / Runekeeper / Guardian, Guild Master of everything but cooking.
Playing now: Hellcat / King Tiger / GW Panther / IS / KV-5 / M4 Sherman and more