Yes I agree completely. The amount of margin required and the vig (premium) make shorting penny stocks very unappealing. I have an Interactive Brokers account, so I can short pennies, but never have for the reasons you post.
I don't see shorting as an issue for CTIX until (hopefully) we are exchange listed and above $5. Any selling we see is likely profit taking, not shorting.
So this pretty much rules out retail shorting. What's left are MMs, and specialist funds, but I don't see CTIX as an attractive candidate for the funds. They want to short quick spikes, not long-term up-trends.
The MMs can be a pain with an OTC stock, no doubt, but just part of the game we have to suffer until when and if CTIX gets a proper listing. It is important IMO is watch their action and stay disciplined in buying and selling to avoid getting sucked into helping the MM make his daily book.