<p>I have a really bent heatbed PCB, the middle is elevated about 3 mm with respect to all edges.</p>

<p>I have found this thread <a href="http://midibox.org/forums/topic/17599-warped-pcbs/" rel="noreferrer">Warped PCBs</a>, where a heating method is applied by baking a PCB in the oven, as described here: <a href="http://www.circuitrework.com/guides/3-2.shtml" rel="noreferrer">3.2 Bow and Twist Repair</a>.</p>

<p>Can this help straightening out a Prusa heatbed PCB? If so, can I apply the heat by the heatbed itself, or do I need to utilize an oven? Will the pressure from the strongly clamped glass plate be enough or will the glass break at these temperatures (given that the heatbed can reach them).</p>

Baking PCB in an oven is not a good idea, I would say. I know PCBs are resistive to the heat (especially heatbeds) but, still, it sounds odd. But the real question is how baking would help. Let's leave it.
If your heatbed is such bent you can do few things depending on your situation/environment.
You can:
Add two glass plates (at the bottom and at the top) and clip them all together;
Support your HB with flat aluminium or even wood;
Add an aluminium frame, or;
If you use glass plate, clip the HB to the glass using stronger (wider) clips.
Ad#1 the thermistor can even stay sandwiched between the PCB and the bottom glass plate.
Ad#2 If your HB is bent up in the middle, you can use the middle thermistor hole. Drill it a bit with fi8mm drill (but not too much, I would say halfway through) and use a cone head screw to screw it flat on to the aluminium/wood support. Of course you will have to install a thermistor into the new place.
The simplest, and less destructive, solution is #1 and I would recommend that.