I'm afraid I'm not terribly familiar with heat moldable insoles but I will say that as a now solution, they could be very helpful. You might want to try to find a set with a metatarsal (MT) button. The MT button sits just behind the ball of the foot and helps to restore the normal MT arch. The button should not be right under your hard spot, but behind it, lifting the bones of the foot upward and relieving pressure off the bad bit.
Other things that help:
1) Moving your cleat back on your shoe. Possibly moving it towards the inner part of the shoe as well, although this can sometimes mess with your knee alignment so it's better done by a fit professional.
2) Making sure you are comfortable on your saddle. More weight through your tush, the less weight you put through your feet.
3) Working on single leg drills to improve pedaling mechanics
As for the orthotics debate, Oak is right, orthotics are in fact a bracing technique and long term will lead to muscle atrophy and potentially stiffness. Having said that, some people have structural change beyond what can be corrected with exercise and mobilization, those people may always need orthotics. The longer you've worn the orthotics, the more likely this is to be true and the longer it will take to regain strength and mobility if you are going to try to go that route. The situation I see most often in my work is that people have weakness and stiffness, they have to use orthotics at least part time to manage functionally but over time they can reduce or eliminate their time in orthotics through diligent exercise. I would say that less than 20% of the people I see fall into the category of having so much structural change that they will need orthotics always.
