I came across a great post from Martin Hatch today, which provides a solution for problems with content types and list definitions in features.
I tested it and it seems to work great, although i did make a little change, since the handler throws an error when using a RemoveFieldRef node in the CT definition.
So, i changed this:
foreach (XmlNode fieldRef in node.ChildNodes)
{
#region Loop through FieldRefs
//ignore XML comment tags
if (fieldRef.Name == "#comment")
{
continue;
}
string fieldID = fieldRef.Attributes["ID"].Value;
SPField field = cType.Fields[new Guid(fieldID)];
cType.FieldLinks.Delete(new Guid(fieldID));
cType.Update(true);
cType.FieldLinks.Add(new SPFieldLink(field));
cType.Update(true);
#endregion
}
to this:
foreach (XmlNode fieldRef in node.ChildNodes)
{
#region Loop through FieldRefs
//ignore everything but FieldRefs
if (fieldRef.Name == "FieldRefs")
{
string fieldID = fieldRef.Attributes["ID"].Value;
SPField field = cType.Fields[new Guid(fieldID)];
cType.FieldLinks.Delete(new Guid(fieldID));
cType.Update(true);
cType.FieldLinks.Add(new SPFieldLink(field));
cType.Update(true);
}
#endregion
}
Seems to work to me, but if anyone has another suggestion 
please do let me know 