Courtney,
Sounds like you are doing the right thing. Marketo does not do math when it comes to lead score, in the sense that it does not automatically add up your behavioral and demographic scores to create your overall lead score. This means that if you increase your prospects behavioral score by 10 points, then you also need to add a flow action to increase lead score by 10 points as well.
As such it sounds like you are doing the right thing. Even if you remove all of your leads lead score, and bring their behavioral score to zero, the demographic score will remain intact, and if you are using demographic score in MSI then you will still be able to see how good a lead it based on their demographic score.
The bigger question is, do you want your disqualified leads to be able to come back to your sales team? In my opinion the disqualified status should only be selected if there is no chance of selling to that prospect. As such, I choose to throw those leads away so to speak. I don't want them coming back later and wasting more of my sales people's time.
For recycling, you want to make sure that they have shown enough interest level again to warrant another phone call from sales. For this reason, I think it makes sense to send them back to square one and go through the process all over again.