Harko I put BTTS because I believed England would score but I often go for BTTS in BSFL for the very reason you gave: knowing my opponent is likely to choose BTTS. Very similar thinking we have in BSFL I've been discovering..!
I think it's always going to be difficult to put down something that's fair for both the person failing to submit, their opponent, and then the rest of the league. I can certainly feel the "pain" of those who never "enjoyed" free points.
'm willing to accept whatever happens, it doesn't really concern me and I'd never feel that any decision is unfair -- everything balances out for everyone in the long run.
I do like a concept that only penalises the offender, and not benefits the other. I agree with cryptofrka, a walkover happens extremely rarely in actual football so that 3-0 reflects that rarity. But BSFL need a way to figure out how to settle the game so I'm okay with this 3-0 rule. Not adverse to a change if someone figures something better.
Slaman29's suggestion isn't too bad actually. It only penalises the offender, and still ensures both teams play a normal game in the following round, no "bonus", just a point penalty + the fee rule penalty. Might I suggest that in the following round, the offender also has to give a handicap? Say, if it ends in a draw, the offender loses. Call it the away goal rule. Complicated though, unless we hope it happens less and less.