This isn't really a problem of the proportional system - given a large party narrowly over 50%, relatively small interest groups within the party will start gaining extraordinary weight as well. Just think of the tea party.
In my opinion, the upside of splitting the parties up is that it makes these particular power struggle more visible, and allows parties more flexibility in ignoring interest groups when a majority can be found elsewhere.
An even more extreme example is Japan: the LDP was in power from 1955 to 2009 (except for two years in 1993-1994), with the result that actual policy decisions (as well as who go the highest political offices) were negotiated between factions within that party.
In my opinion, the upside of splitting the parties up is that it makes these particular power struggle more visible, and allows parties more flexibility in ignoring interest groups when a majority can be found elsewhere.