I've seen this same conversation over the years. Another approach I've seen to taking possession of the physical certificates (which I've heard is a solid idea) is to put your shares up for sale at a price much higher than current asking. Shorting cannot be done to shares placed in escrow in a selling account. A few years back when Tahera was being explored the shorters were constantly screwing with it... until a grassroots effort took millions of shares out of reach by posting them for sale at 10x market price.
The catch... Some brokerages won't take sell orders for more than 50% greater than current asking price, while others don't seem to have a limit. I used to keep track of which brokerages were unlimited (eTrade was before Scotia Bank too over in Canada, now I'm not sure). A little experimentation would show whether your particular brokerage had a limit or not. If you can only put up at $3 with your brokerage, then that's not a very safe approach with SLI, IMO.
But, if it turns out you can put your shares up for sale at $5000 each, they should effectively be short-proofed. You would also have to remember to renew your offer when it times out - generally an offer is good only for 30 days or so at most brokerages.