Learn English – “But Only” – How to Figure Out the Meaning

"I was only..." implies that the outcome went beyond, or differed from, the intent: "only trying to help," "only saying x and y," etc. The "but..." is implied because of that conditionality. The word "only" limits a statement to a specified context.

I think it goes a little further though: "but..." isn't inherently negative. The backhanded feel likely comes from the dissonance in the word "only." —"you were only trying to help" rarely means that the other party did more good than was intended. The word "only" reiterates and emphasizes the fact that the outcome differed from the intent or expectation.

Depending on context, "only that" as a transitional phrase can mean several things. Consider this extract from Rhys Prichard, "Advice and Warning to the Adulterer" (written by 1644), published in The Morning Star, or Divine Poems of Rees Prichard (1815):

Thou goest like a fool, to sell thy soul,/(Thy soul, for which thy Saviour deign'd to die!)/The grace of God, and all the joys above,/Only that thou may'st with a Strumpet lie.

O, do not deal so hardly with thy soul,/Give it not to be torn by fiends in hell,/Only that thou in those base joys may'st roll/On which all carnal minds with transport dwell!

In both instances here, "only that" means something along the lines "for the sole purpose that."

In contrast, Henry Mackenzie, The Man of the World (1773) reprinted in The Works of Henry Mackenzie, Esq., volume 8 (1808) has this:

She seemed unconscious of my approach, though her eye was turned towards me as I entered ; only that she stopt in the midst of a quick and lively movement she had begun, and, looking wistfully upon me, breathed such a note of sorrow, and dwelt on it with a cadence so mournful, that my heart lost all the firmness I had resolved to preserve, and I flung my arms round her neck, which I washed with my bursting tears!

Here, "unless that" means (matching the meaning that Kris suggests in a comment above) "except that."

Lennox Robinson, from an unidentified play in Plays (1928) [combined snippets] offers this:

PETER. Oh, it's nothing very much. Only that a couple of chaps have left the office, and there'll probably be a re-shuffle of posts.

MARY. It's only that Peter will probably have about twice as much as he has now; it's only that he'll be able to marry you at last, my dear.

Here, "only that" means simply "nothing more than that."

Emily Lawless, Grania: The Story of an Island (1892) has this:

The silence everywhere was extraordinary. The sea under its close-fitting shroud seemed as absolutely unruffled as the basin of some indoors fountain. Not a ripple anywhere ; only that same slow internal movement, a movement hardly to be perceived upon the surface ; only the the gradual undertow of the tide drawing everything stealthily in one direction.

Here, "only that" can be understood either to mean "nothing more than that" or (with a stronger sense of contrast) "instead, that."

And Edmond Gastineau, Edgar Livingston: A Story of New York (1897) has this:

Edgar had accepted the sacrifice; he had yielded to the fateful destruction. Only, that sentiment which he believed crushed within him had asserted itself, though he knew it not, and it was this which had made what he had said to her so strangely empty and meaningless.It was this which left him dissatisfied and wondering.

Here, "Only, that" means "However, that."

In the OP's example,

This does not mean that it is freely chosen, in the sense of the autonomous individual, only that there is popular agency in the hegemonic valuations of marketplace society, unlike in customary and command societies.

"only that" seems to mean, as tchrist suggests in a comment beneath the question, "rather, it means simply that." Expressed at greater length, the sense of that sentence is approximately as follows:

This does not mean that it [a particular price, presumably] is freely chosen, in the sense that an autonomous individual might choose something; rather it means simply that popular agency is at work in the hegemonic valuations of marketplace society, unlike in customary and command societies.