It is extremely hard to put an estimate on this.
Firstly it's impossible to know how many civilians he killed (probably unwillingly) during battle, so I will just ignore that.
Then your wording implies that you consider all civilians in-guilty or undeserving of the death penalty; Some states of the US have a different opinion.
It is generally agreed upon that Che had an ulitarian view - If it helped the revolution the death penalty is correct (Anderson 1997, p. 375, Castañeda 1998) ("The situation was uncomfortable for the people and for Eutimio so I ended the problem giving him a shot with a .32 pistol ..." as described in "Death of a Traitor")
http://en.wikipedia.org/wiki/Che_Guevara#cite_note-114 gives an first estimate over his death-toll during his bureaucratic days.
He ordered 105 or 144 (Discrepancy is explained in the link given, IMO 144 counts) over complete Cuba, of which 104 were in the prison he oversaw.
From January 59 to June when Guevara left Cuba as "Diplomat" (and thus gave away his administrative powers) 200-700 people were killed all over Cuba, many not by order of Che.
However you question was how many of those were civilians - prisoner during that time included officals of the old Batista goverment/regime and traitors (to the revolution).
Some of the civilian officials were corrupt and tortured or killed the opposition.
The army did only defend itself against terrorist seeking to overthrow the goverment and establishing the Ley de la Sierra which had the death penalty as a cornerstone.
Then there was the time during the actual rebellion - the rebells established the Ley de la Sierra which had the Death Penalty as a cornerstone. A famous example is Eutímio Guerra.
Records from that time do exist in the cubaarchive.org (from all times actually); To get an estimate I did an advanced search with "Batista Regime" and "Death atttributed to: Castro Rebel Army" - that gave 371 more cases. It isn't clear how many of those are attributable to Che himself. (I guess one could automate looking up the case id and if "Che Guevara" appears in the Case description would count as one more confirmed kill)
However it think it is quite clear that 14000 is just plain wrong and a reasonable amount would be around 200.