I don't know how to select faces of a brep, but if you can figure out their index in the Rhino.Brep.Faces list then you can use:
Rhino.Geometry.Collection.BrepFaceList.RemoveAt()
This seems to work here:
Code:
import rhinoscriptsyntax as rs
import scriptcontext as sc
import Rhino
brep = rs.GetObject('pick brep')
rBrep = rs.coercerhinoobject(brep)
#to check face list
for face in rBrep.Geometry.Faces:
print face
#remove a face from the face list
rBrep.Geometry.Faces.RemoveAt(1)
#make a new brep by duplicating the original but now has 1 face deleted
newRBrep = rBrep.DuplicateBrepGeometry()
print 'CHANGE'#just to break lists
#to check face list of new brep...should be -1
for face in newRBrep.Faces:
print face
#this replaces the original brep in the document with the new on without the face
sc.doc.Objects.Replace(brep, newRBrep)
#redraw views
rs.Redraw()