Looks like the easiest solution is to count down the auto seconds 1s at a time instead of 500ms, but that would mean you can't have 6.5 second autos. Personally I think autos should be reduced to 6 seconds and manual attacks raised to 6 to match it so it doesn't punish people as much for spending their credits ($$$) on autos. If you're not interested in doing that then please consider using webworkers to make it work with 6.5 seconds.
i favor autos reducing to 6.5 seconds. and running BoL in the background at lower speed is really an issue that should be addressed right away, i used IE tabs but there were times its still slow as usual.
Webworkers is not an option. They have poor compatibility and very poor performance. In addition, changing the timers would result in a degraded experience when in tab and it would require a massive amount of code changes. This is not a priority as of now. I may add this down the road but running the game in it's own tab accomplishes the exact same behavior with zero code changes, allowing other features to be added.
Not sure how it's done here, but for such purposes I have used a socket server (socket.io) which executed the timer on server side and was updating client with the remaining time (in realtime). You can either update the client manually or automatically (either in realtime or in a specified intervals), or update the client when the tab goes form passive to active mode.
It's worth mentioning that Having the timer executed on server side has some advantages.. but it may also slow down the server's performance for a little bit.