Totally irrelevant, and something that no one will remember. After all, it occurred at a house show, and was not recorded by WWE cameras. So I would not expect any attention whatsoever to be d rawness to it outside of this one particular house show.
Plus, we don't even know the context of the statement. For all we know, the fan was wearing a TNA t-shirt, and elicited a spontaneous comment for this reason alone. I wouldn't be too quick to read any deep hidden meaning, or any particular significance, into this isolated incident. After all, why would CM Punk, near the top of he heap in WWE, bother to call any attention, positively or negatively, to TNA?