Thomas, younger brother of Caerphilly fly half Justin Thomas, has amassed 250 points this season, while Freeman from Llanelli Under-21's has run in 13 tries.
Their places go to fly half Paul Fisher and wing Nick Jones, while centre Emyr Jones has received no suspension for a recent red card and is included in a side skippered by the former Wales lock Paul Arnold.
There is a doubt over prop Ben Grace and former Wales tourist Aled Griffiths stands by at loose-head, while Wales Under-21 cap Gareth Williams will be at flanker, on dual registration from Llanelli.
Quins: B Thomas; N Jones, D Simpson, E Jones, A Rees; P Fisher, S Wake; B Grace/A Griffiths, E Evans, M O'Kelly, P Arnold (capt), P Matthews, S Jenkins, A Mason, G Williams.
Replacements (from): B Grace/A Griffiths, J Hughes, D Niblo, P Beynon, P Morgan, Deiniol Evans, G King.