Old website has lots of index.php URLs indexed. How to redirect?

I just found out the hard way that Magento will redirect anything with index.php in the URL straight to the home page if you're using SEO friendly URLs. The issue is that we have an old website that has a ton of URLs indexed that look like this: /index.php?route=product/product&product_id=70

So 301 redirects in the htaccess file do not work and I also tried adding the URLs to Magento Admin's URL Rewrite Management with no luck. Is there any way to make this work?

Example, this is what I'm currently doing that doesn't work thanks to the index.php:

Code:

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redirect 301 /index.php?route=product/product&product_id=70 http://www.bosu.com/bosu-sports-conditioning-football

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Just do this way

Code:

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# Redirect old file path to new file path
Redirect /olddirectory/oldfile.html http://example.com/newdirectory/newfile.html

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You don't need to put 301