In the Mission Earth dekology (published 1985 - 1987 posthumously), criticism of psychology is a common theme. As is criticism of corrupt power holders and drugs.
Battlefield Earth (1982) explores the exploitation of the banking system for extreme profits and once again, he attacks psychology with the use of the Psyhclo Catrists who use implants and surgery to turn the Psychlos into violent sociopaths.
Both of these works are written well after Scientology gained a foothold and he is very careful not to directly include references to his religious beliefs in his science fiction works. However, it is almost certain that he used his church to bolster sales (link) and in the case of 'The Church of Scientology vs Gerry Armstrong' (1984) Judge Paul G. Breckenridge ruled in favor of Armstrong's biography of hubbard stating:
The evidence portrays a man who has been virtually a pathological liar when it comes to his history, background and achievements
Taking these points into account it can be inferred that he did use his later science fiction works as a tool to further the cause of his Church.
According to the plot description in Wikipedia on his fist novel; Buckskin Brigades (1937) (well before he wrote Excalibur which is supposedly an unpublished precursor to Dianetics) it would seem the theme of corrupt evil power holders is explored.
Unfortunately, I have not had the opportunity to read any of his early pulp fiction works so I cannot comment on their content.
As for recommended reading order; that would depend on if you are interested in the Church or his Science fiction works. I cannot comment on recommended reading order for his religious works (your local Scientology church would be happy to advise you on this). For his science fiction works I would start with Battlefield Earth. It received scathing reviews but it was one of his better books and at least it is not 4,000 pages long.