Yeah, it sucks to have a game cancelled after you've spent a couple minutes pondering the initial set-up, but I'm not sure this is a big enough problem to warrant the changes you are suggesting. It's only happened to me twice out of the 20 or so games I've played.
I think this problem will work itself out as more people play 960 and decide if it suits them or not.
Chess960 is designed to provide an unpredictable starting position, within limits. All of its unique advantages and disadvantages stem from that feature, and people who choose to play it rather than standard chess do so for that reason. Any system which allows a player to predict the starting position therefore subverts the spirit of the game.
Chess.com allows a player to cancel a game within a small number of moves. This seems like a reasonable policy for normal chess, but it has peculiar implications for chess960:
Any player can start a bunch of games and selectively choose only those starting positions which match a given set of criteria. For example, a player could devise strategies which only apply to games with bishops on the same side of the board, and then selectively play only those games to which the strategies apply.
This doesn't seem like a big deal by itself. If those players want to reduce the variety in their games, they can do it. Maybe they'll gain a slight advantage in preparation, but people with more free time on their hands have a similar advantage. These hypothetical chess960 players are just like players of normal chess who always play the same opening, or the same defense to a given opening - except for one thing. In chess960, the first move requires much more thought than in normal chess. A player might generate a complete strategic system from scratch for a particular chess960 setup, before making a single move. This time investment is much higher than it would be in the opening of regular chess, and if one's opponent cancels the game, one cannot simply start a new game with the same initial setup.
Because the loss for the player whose opponent cancels is uniquely high in chess960, I think we should consider eliminating the 'abort game' option for new chess960 games, at least after enough time has passed that people stop accidentally starting chess960 games when they intend to play regular chess.
I use the word "consider" because I want to initiate a discussion. If somebody has good reasons why the 'abort game' option is useful for chess960, I would love to hear them.
Even if the option remains officially avaliable, I would also like to encourage players to weigh the investment of their opponents before choosing it.