One thing I always do is add an orthotic insole to my running shoes - as soon as I get them. Sometimes I have to take out the insole that comes in them, and sometimes I can just fit the orthotic one in on the bottom and add the running shoes' one on top - it just depends on how much room you have.
This adds extra support and cushion, and I have learned over the years that is just pays to go ahead and put them in right away. You can find them Walmart, Target, or you can order custom made ones online or from your podiatrist. The picture looks like a pair I have used with alot of success
I think the run/walk program you are doing is good, and I know it must be hard for you to hold back, since you have been a runner in the past and have run a marathon - but just be patient - as the weight comes off and you build up strength and endurance you can run more and walk less.
Remember, you don't run to get fit, you get fit to run. (Very hard for a runner to accept! - trust me, I know! lol) Losing weight first with controlled, careful but purposeful exercise will allow you to get back to where you want to be, so you can enjoy running, or whatever you like, without the worries of unnecessary injuries.