TheMadScientist - 1:02 am on Dec 19, 2012 (gmt 0)
I wouldn't worry about it, as long as they're no longer linked or causing an 'annoyance' to visitors, which it doesn't sound as if they are.
If WMT wording was a bit better I think things would be easier for webmasters to understand, like if they simply switched 'warnings' to 'notices' it would likely be interpreted in a totally different way than it currently is.
'Warning' seems to say 'there's something wrong' or 'cause for concern' inherently, but a 'notice' is much more likely to be interpreted as: 'Hey, we saw this, did you mean to do it, or do you need to correct it so we can get to the URLs and rank them again?'
Obviously, in your case, the answer is the second portion of what I think a notice would be interpreted as, and forbidding Google from accessing a URL you would like to keep for internal use should not cause a problem for SEO, as long as that URL is not linked and/or causing an annoyance for regular visitors.