Can a faulty throw out shaft bearing cause the input shaft of transmission to break?

It's very unlikely that a failing throwout bearing will damage the transmission input shaft. What's more likely is that the clutch fork, the part that moves the bearing itself, could be damaged.

I recommend getting this fixed (or fixing it yourself) as soon as possible as it can fail totally without warning and at the LEAST convenient time.

The knocking noise is almost certainly the bearing itself. By the way, it's usually a good idea to replace at least the clutch plate and possibly the pressure plate and the flywheel at the same time. Most of the expense is getting the transmission out and all those parts will probably be worn too.