I hate conversation mode. I agree with Svafa (a few posts back) about it being terrible with e-mailing reports from cron jobs. I used the exact same soluton; timestamps in the subject. I still use Thunderbird + IMAP though since I can't (easily) view messages in plain text in GMail.
The conversation filtering is so intrusive and crappy at what it does that it should be considered a bug, not a feature.