kodiak1,
I fillet everything I catch. It usually takes me about 1 minute per fish to fillet. On a good day I can get that down to maybe 50 seconds but that's about it. When filleting kokanee, I like to take the skins off because then I don't have to deal with all the scales. The actual skin removal takes me about 6 seconds per side but, before I can do this I must first split the two fillets at the belly and remove the belly fins. By the time all steps are made, I expect to be done with everything for each fish in about two minutes per fish. Not sure how this stacks up with your current way of cleaning fish but I find it to be pretty comparable with any other way I've seen. Timewise that is. I'm hoping that someday I will be able to talk somebody into videoing my fillet technique so that I may share it with others. It is a little different from the way I see others do it and, in my own opinion at least, a little better.
I have never had a problem with pin bones on a kokanee, but then again, I've never caught one much over 20" either. I would guess that about 20" is when you're going to start to notice the pin bones in them. I usually fry my kokes in veggie oil and corn meal and this way the bones definately are unnoticeable. I also love to eat them grilled over an open fire, and this way too the bones are no problem. I have only occassionally had them smoked since I usually manage to eat them too fast for such an opportunity but, the pin bones were no problem then either.
I can only speak from my own experience but, if you do a good job with the filleting, you should have no problem with pin bones on kokanee at least up into the 16" to 18" range and probably not until they get over 20". I'm pretty fussy about my fish and have an even fussier family to provide for, they too have all given their approval of not worrying about the pin bones. The best thing I can say is give it a try and see what happens with that first batch. You will learn with experience what to look for in the size of bones that you will need to worry about. Trout and kokanee have fairly light bones up to the 20" mark and you should be safe to there. But you can always rely on the way they used to do it, always eat bread with your fish so it can chase the rare stray bone down as a "just-in-case" back-up plan.