Maybe what you're looking for is summarization to a more inclusive taxonomic level? For example, the case you give above looks like you've summarized to the species level (level 7), so that Enterobacteriaceae__g__s and Enterobacteriaceae__Serratia__s end up as separate lines on the summarized OTU table. But what I infer you're wanting to do is to get everything assigned to the family Enterobacteriaceae rather that to more specific genera and species. To do that you'd simply filter your starting OTU table at a different level. Per Antonio's code:
filter_taxa_from_otu_table.py -i otu_table.biom -o f__Enterobacteriaceae.biom -p f__Enterobacteriaceae
This will give you all OTUs classified as Enterobacteriaceae, including those under Enterobacteriaceae__g__s and Enterobacteriaceae__Serratia__s
does this make sense?