@Pseudonymous
From his job jumping in his early days to his subsequent career in theatre, to his postwar migration to folk I get the very clear impression that he was a bit of a control freak and had always retained his independance. Just my impression but it would certainly create a problem for him when conscripted(as you point out) He had also been an activist from the age of 17 when I believe he participated in the Kinderscout trespass.
A few sources gathered in no particular order:
From: Joe_F - PM
Date: 13 Dec 09 - 06:35 PM

23 Aug 39: Hitler-Stalin pact
01 Sep 39: Britain enters war
24 Jul 40: E.M. conscripted
18 Dec 40: E.M. declared a deserter
22 Jun 41: Germany invades USSR
08 May 45: War in Europe ends
16 Dec 46: E.M. arrested
ca 11 Feb 47: Court martial canceled on medical grounds
26 Feb 47: Moved to hospital
10 Apr 47: Released,
----------------------------------------------------------------------

An entry in 1940 from the Commander of the 11th Battalion, King's Regiment, encloses a copy of the song Browned Off with which the young Miller had entertained fellow troops, and included the commendations "appeared to be a very good soldier of more than usual intelligence" and he "was NOT a grouser, and always appeared cheerful and willing".

Just two days later, MacColl deserted.


But MacColl's talents also earned him praise from police. In January 1939, Lancashire constabulary noted of his performance at a rally that he "showed exceptional ability as a singer and musical organiser". A note to the Chief Constable of Blackburn a year later, advised "in present conditions, it would probably be advisable to dissuade the town clerk from granting any future application from Theatre Union if it is made".

and
.his commanding officer expressed his concerns to Hyde Borough Police on December 16, 1940.

The report stated: "His influence over his fellow soldiers was that of a man of much greater intelligence than the ordinary soldier.

"In some ways they would follow him, though at no time was he ever discovered suggesting improper action, he may well have done so under cover. "

Two days later MacColl went AWOL.


In January 1941 a colonel wrote: Pte. miller has been absent from this unit without leave since 18th December, and there would appear to be something fishy concerning his absence, as communications have been received from his wife asking for extensions of leave.


https://newhumanist.org.uk/articles/995/sandals-and-spooks

http://news.bbc.co.uk/2/hi/uk_news/4772328.stm

What happened during the war years is a bit of a blank,but it is surprising that MacColl was reinstated with the BBC so quickly, bearing in mind the authorities being so wary of him. That is an avenue that could do with researching.

A lot is made of him leaving school at 14 but The first major raising of school leaving age, a formal change in school leaving age policies occurred in 1939. Parliament debated to raise the age to 15, although this was delayed due to WWII and not formalized until the Education Act of 1944 and implemented until 1947.


https://www.artangel.org.uk/did-you-kiss-the-foot-that-kicked-you/ewan-maccoll-a-man-to-be-watched/

More on his arrest and dismissal on psychiatric grounds from:
Joan Littlewood's Theatre

https://books.google.ie/books?id=u4NsNL9XZ5MC&pg=PA57&lpg=PA57&dq=maccoll+court+martial&source=bl&ots=fi-cS9VB8U&sig=ACfU3U1Hcze

A man of many parts, British folk singer, songwriter, communist, labour activist, actor, poet, playwright and record producer.

Like everyone else he had a few warts and could sometimes be obnoxious, most seem to recall him positively.
I wonder what history will primarily remember him for?