I think second option would be too much confusing for users who are used to use single click or double click.
I tend to lean towards the first option (no hiding with a click). I like that you can quickly open and hide roster window, though i use it very rarely. Most of the users will only benefit from that. But we can piss off a few power users who actually use it to quickly glance at their roster and hide it without having to move a mouse to click the X button. I hate to introduce another option. But maybe this is a better way. We have Preferences > Login:
"Use single click in system tray to bring spark to front"
We can have there something like "Clicking in system tray never hides spark window" or "Clicking in system tray always brings spark to front" and it can be even enabled by default, so power users would only have to uncheck it. More work (adding new line to i18n file and option code), but maybe more liberal.
I will ask Konstantin too. We can have a poll on the start page about it, but from my experience only a few people care to vote