I believe they start at 75%, but your point still stands. You get given the benefit of the doubt when you're new, but having good karma is not a reason not to kick. Every player who plays too slowly has to start doing it somewhere, and people have the right to assign penalties as they see fit (within what the system allows - ie. if you're over time, your opponent can choose to penalise you, and is not in the wrong for doing so).
This has been discussed before and there is a suggestion (bug report) somewhere specifically for Ark Nova requesting that more time be given in these situations, which you can go vote for. However, the BGA system as it currently stands means this is not a simple thing to do and would need some changes in the framework.
That said, in your game of Ark Nova, it didn't look like it was the double move that caused the issue (although you were playing two animals), but rather the fact that you didn't start the actions of your turn until you were down to about 20 seconds of positive time (after starting the turn with 2:45 on the clock). Maybe you were thinking about your move, but that's part of the game to make your move and your decisions within the given time. Else, choose a slower speed.
And while I say that, I personally don't usually choose to eject a player who is actively playing as I'd rather play a game than not, and I do find it somewhat annoying when others do (in a multi-player game that I am part of). That said, players are within their rights to do so, as has been stated. The rules are what the rules are. If no one can ever be booted, that would cause problems. Auto-booting means people like me who'd rather play than not would be more frustrated. To be honest, I don't see there's a way they could change ejection settings to be "fairer". As for time limits, well, there's a decent range of them, so if you want more time per turn you can choose that too. If you want more time options, I believe there's suggestions in for those as well, which can be voted for (though I think the most popular of these is for a faster turn speed than fast), or you could raise one yourself. Apart from that, you can't do much else other than choose your time limits to suit your play.