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A leaking junction block will not damage the master cylinder, however if you applied the brakes and the master cylinder piston traveled further than normal into the bore it could be toast. You will know once you have bled the system and see if the master cylinder holds. Bleeding the system using the master cylinder always put it as risk for the same reason- seals can be damaged by forcing them into territory not previously ventured into. Pressure bleeding is much preferred.

In preparation of changing out the junction block: Use a wire brush to clean off as much rust and crud as possible from the block and fittings. Make many applications of penetrating fluid on anything you want to move. Real penetrating fluid as in Kroil or PB Blaster. Keep it wet with it and scrub it with the wire brush, dental picks, whatever will help remove the rust externally and allow the fliud to lay at the points you want it to penetrate. Use a high quality line wrench when it comes time to actually remove the lines into the block.

Good luck.

Randy