Rather than change the module, the solution can be achieve easily in the templates.
Firstly, on the page edit keywords screen, choose a character that you know will never be used in the meta section. In the example below, I've chosen the tilde character (~).
In your template, capture the SEOTools2 module and assign it to a var. Then put the var in the template with the replace modifier. Replace the ~ with a space.
Example:
Keyword edit screen:
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rubbish garbage keywords these~keywords~should~be~grouped
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{capture assign=seo2}{SEOTools2 showbase=1}{/capture}
{$seo2|replace:'~':' '}
HTML output:
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<meta name='description' content='This page covers the topics rubbish, garbage, keywords, and these keywords should be grouped' />
<meta name='keywords' content='rubbish, garbage, keywords, these keywords should be grouped' />
psy