I'm not an expert in this subject but I'm think I agree with connectegr. Assuming the connection is only located in a few areas my advice would be to remove the seat and then add plates or angles as needed to get the design you need. At any rate by removing the seat you would know three things that would help make your problem simpler.
1) You would know that the connection is not transfering any moment, and all shear is going through the tee part of the connection.
2) You would know that you only have to design your moment plates for live loads in the structure whether they be floor live loads, roof live loads, or seismic live loads. All dead loads are all ready being transfered in simple shear. This helps you in not overstressing the columns. Hopefully your live moments are less than your seismic load moments.
3) You don't need to analyze the tee connection anymore as the moment will be handled by the added on plates.
Assuming you don't have a lot of P-delta issues in your frame analysis you could superimpose the dead load case onto the other cases and see if your columns work as if the connection were traditional moment connection. If that didn't work than you could size the plates or angles just right so that they would qualify as a flexible moment connection.
If by removing dead load moments your column overstressing problem is solved than you could probably get away with just removing the bolts from the seated connection and then replacing them. It would be like releasing the dead load moments from each end one at a time. Friction might prevent this though.
Living in Florida I don't have to deal with the seismic requirements thank God. I honestly don't know how you can make ends meet dealing with all the seismic provisions but that is another story. For me wind is enough. And I'm still not yet comfortable with the whole flexible moment connection idea to be honest. You would really have to do it just right and have really good inspectors in the field. In my practice I either assume its a moment connection or simple shear. Of course this doesn't help you situation out much.
I agree with other comments above also that we never really have a pure simple shear connection unless of course we one bolted everything. I always try to be conservative with my columns. This was a fun question to think about and I'm glad its not my problem. I've gotten to a point though where I'm tired of trying to do physics gymnastics trying to justify things I'm not really sure about. Hence my advice above. Do something that makes this problem simpler and lets you sleep at night.
John Southard, M.S., P.E.