Unfortunately it will likely have a negative effect no matter what you do. The effects though are temporary. If you MUST change the URLs, and you CANNOT 301 redirect the old URLs to the new URLs, you will risk your rankings, period. At least short term.
No Index, no follow on the old is not going to help. You might try creating a custom 404 page that 301 redirects to your home page. This is not nearly ideal, as your old section pages were targeted and your home page is not, but at least your keep any backlink credit in the family so to speak.
If most of your external backlinks point to your home page and product pages, you should regain your rankings before too long. If many are pointing to the pages you are removing (changing the URLs of) I strongly suggest you create 301s at least for those with lots of external backlinks.
Finally, make sure you run a headers checker on your new set up to check that old urls are redirecting correctly with 301s not 302s. Make sure to double check everything.
However, do take your time to read everything you possibly can about 301s. It's easy to get confuse initially, but makes good sense with time.
The home page may experience a short-term negative effect. However, assuming there are no links from external pages to the pages lost, the new pages will get indexed and provide the same internal linking value as the previous pages. Thus, no long term effect to the home page.
Best of luck!
Changing Your Site's Url Structure. How To Avoid Your Site Being Penalized - To learn more about this author, visit Serge Daudelin's Website.
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