It had a specific nautical meaning in the 19th century. From the OED:
I. 35. †f. Naut. In the imperative phrase make it so, by which the commander of a vessel instructs that the time reported to him (e.g. the end of a watch and spec. noon, when sights are taken to determine what was formerly the start of a ship's day) is relayed to the crew (see quots. 1826 and 1867). Hence (occas.): to mark (a time of day, etc.) formally in this way. Also in extended use. Obs.
1826 Let. 14 Mar. in G. Jones Sketches Naval Life (1829) I. 101 Eight bells are now reported to the quarter-master, and by him, to the officer of the deck; who answers, ‘make it so’; and sends a midshipman, to inform the captain, that it is meridian. The bell is struck; and two long successive pipes, from the boatswain and his mates, are the signal, that all work is to cease.
V. To behave, act, or move (in a specified way).
a. [Probably after the same Latin idiom as sense 55a.] to make it (with adverb or adverb phrase of manner): to act, behave. make it so: see also sense 35f. Obs.
eOE King Ælfred tr. Gregory Pastoral Care (Tiber.) (Junius transcript) xvi. 98 Ðeah he [sc. Paul] upaðened wære on his modes scearpnesse, ne forhogode he ðæt he hit eft gecirde to ðæm flæsclican burcotum, & gestihtode hu men sceoldon ðærinne hit macian.
a1586 Peblis to Play in W. A. Craigie M*aitland Folio MS* (1919) I. 178 Quhat neidis ȝow to maik it sua?
I found an example earlier than the OED's 1826 of the naval command. It appears in correspondance in The Naval Chronicle, For 1808: Containing a General and Biographical History of The Royal Navy of th United Kingdom; With a Variety of Original Papers on Nautical Subjects Volume XX (From July to December):
THE grand mechanism of naval discipline (if I may be allowed
the expression), consists in the various gradations which
take place, from the monarch who delegates his power to the
Admiralty, to the lowest ship-boy. [...] This
rule is in general well supported in our ships of war, and it has
amused, if not excited the ridicule of some landmen who have observed its various stages
in trifling instances. Thus, a centinel
informs the quarter-master, that "it is twelve o'clock;" the
quarter-master the mate ; the mate the lieutenant; the lieutenant
the captain ; the captain the admiral ; and then the order to ring
the bell, or, as it is usually, though absurdly, expressed, make it so,
returns back through the same number of persons, before the
important command can be given to, and executed by the cook's