Is there a rule against using filtered images?

No,* although I was referring to why the image as-is wouldn't be used. Images sometimes undergo minor editing for things like color correction, watermark removal, etc. It'd be preferable if the original image didn't have the red eye, but the correction isn't a huge deal. The poor lighting is the much more severe issue.

* There are different levels of "rules" on the English Wikipedia. I'd categorize them into "policies with legal considerations", policies, guidelines, the Manual of Style, and norms.

• Policies are widely accepted Wikipedia standards everyone has to abide by like "verifiability"; the ones with legal considerations are even more serious like "libel".
• Guidelines, like "offensive material", are best practices supported by consensus that editors weigh when making decisions. Often more specific than policies.
• The Manual of Style does what it says on the tin and answers your question about red-eye correction. It's concerned with nitty-gritty technical stuff like when to use certain punctuation, how long a lead section should be, etc. Everything everywhere must abide with few exceptions, although the MoS is so extensive that things slip through the cracks all the time – usually inconsequentially.
• Norms are informal standards outside of policies and guidelines that editors (sometimes only in a specific subject field) usually agree on. As a specific example, most major cities of the world have a collage showing different landmarks, but this isn't written anywhere. Wikiprojects (collaborations over a specific field, e.g. astronomy) often have their own best practices for their specific fields. And there are "essays" – which are opinion pieces editors can easily link to that often describe norms (they don't have to; they can just be an editor's pet peeve) but which aren't binding. A classic example of the essay is about "coatrack articles".