For that type of analysis, I have good experience with Agilent's PLRP-S columns (1000A), ran with a water/acetonitrile gradient (with some formic acid) at elevated temperature (70 degrees Celsius).
Yes, then I guess I'd try HP-SEC coupled to MS. I'm not sure if you worried about protein denaturation at elevated temperatures; the organic solvent will induce that too.
Depending on your question/goal, you could try to include acetonitrile in the SEC running buffer (together with some volatile salts, such as ammonium acetate) or got for a native approach, with volatile salts only.