How will the free update to Mountain Lion work? I am planning to buy a MBP 13" in the coming days. Although as soon as I buy it I will remove its HD and replace it with Crucial M4 256 SSD. Will that stop me from getting free update to ML? 

If so, backing up the HD on TM and then restoring from that on SSD would solve the problem ?
I suspect it will be serial number based, or model number based.  As the new models will no doubt all have serial numbers and indeed model identifiers (iMac 9,1 for example) that will allow them to clearly identify which machines are applicable, and allow the upgrade as appropriate.

In previous "up-to-date" schemes it has been this way, and not reliant in any way on what is installed on your drive.

If you are transferring to a different boot volume, I would recommend using an image file rather than Time Machine.  You can pick up a USB enclosure for your SSD, image the existing drive onto it, and then simply swap them over - this is how I have done things in similar scenarios.