Is that solely speculation or do you have something to support it? Because here's the law in place at the time - Link - and there's nothing in it about citizenship for soldiers.
If Soetoro had another nationality, his work as a geologist for the Indonesian Army would enable him for naturalization under Article 6 of the law you linked. His wife & (alleged(ly adopted)) child would then have an opening to claim Indonesian citizenship as well.
(1)The citizenship of the Republic of Indonesia because of naturalization is acquired with the validity of the decree of the Minister of Justice who grants this naturalization.
{SNIP}
(5)The decree of the Minister of Justice which grants naturalization is valid as of the date that the petitioner takes an oath or swear allegiance before the Pengadilan Negeri or Representation of the Republic of Indonesia at the residence of the petitioner and is valid retroactively the date of said decree of the Minister of Justice.
The oath or allegiance swearing is as follows:
“I swear (promise): “that I release entirely all loyalty “to foreign authority; “that I recognize and accept the highest authority “of and shall be loyal to “the Republic of Indonesia; “that I shall uphold the Constitution and other laws of “the Republic of Indonesia and “shall defend them faithfully; “that I bear this duty out of my own free will “and shall not diminish whatsoever”.
(6)After the petitioner has taken an oath or sworn allegiance as mentioned above, the Minister of Justice publishes such naturalization by inserting his decree in the State’s Paper.
(7)If the oath is not taken or allegiance not sworn within three months after the date of the decree of the Minister of Justice, said decree will automatically become null and void.
Article 6.
Naturalization may also be granted for the interest of the State or because of services rendered to the State, by the Government with the approval of Parliament. In this case from the provisions of article 5 only those in para 1, para 5, para 6 and para 7 are applicable.