Its probably easy to give a feature to allow or disallow HTML/flash tags(if you don't want HTML for other vulnerability reasons) in sigs. That way, you could have both of best worlds. Those who don't like it could turn it off yet still have normal sigs display and those who are fine with it can have it =O
Also, theres very little you could do to block laggy flash apps server-side. If it's running slow, it's a) written in AS2 b) overusing the filters/advanced graphical properties and/or c) coded in a horrendously laggy fashion. If the person making the sigs knows what they're doing, lag generally isn't a problem. If someone has made a sig but it's lagging, I should be able to help them fix it =P