I don't know if Emmitt in his prime would have done any better than Murray with the 2011 and 2012 Cowboys OLine.
The facts are.
Emit Smith is recorded as the most productive RB in the history of the sport in rushing yards and TD's. 2nd all time in TD's by all players only to Jerry Rice.
More facts:
Emmitt Smith had a 15 year career and has only surpassed 1613 rushing yards twice in a single season. Furthermore Emmitt has surpassed 16 rushing TD's in a single season 3 times also in that same span.
More facts:
Throughout the majority of Emmitt Smith's career he ran behind multiple pro bowlers across the o-line.
Just my opinion:
Emmitt played on way better teams than Alfred Morris has in Washington and that will probably remain the case throughout the rest of Alfred Morris' career.
To compare anything Murray has done in any circumstances to Emmitt Smith is lowly quantifiable. However, the 1 season Morris has had would rank as a 3rd or 4th best overall season for Emmitt Smith. Possibly the greatest running back of all time and my all time favorite Cowboy.
The OP and question was Murray vs Morris and although I see your point of explaining Murray's less than desirable circumstances behind our o-line, Washington's isn't known to be anymore dominating than ours. Since Trent Williams has been drafted there has only been 1 pro bowl selection from that line and that was last year and it was Trent Williams.
Morris definitely over Murray if I had to choose today.