At first, I found it very annoying, but I have gotten used to it, and have sort of learned to live with it. I definitely think this should be an option; turn it on if you like it, turn it off if you don't.
What is there to live with? If you don't want your code folded, don't click on the little fold buttons/markers/whatever.
It so happens that I never use code folding, but it never annoys me when it is available. I find it extremely easy to not click on the fold thingies (though I should mention I am not an Eclipse user, and the folding I am familiar with is little plus and minus signs in the margin, between the text area and the line numbers--maybe some other schemes are more intrusive).
However, I believe it would be easy to make a fold-disabling option. The easiest might be to have a setting which hides the markers. For me, the most important setting to have is one which allows all files to be opened with blocks already fully expanded, though I think this is the typical out-of-the-box behavior for applications which have folding.
For people who actually use folding, maybe they would like to have more complicated preferences, like "open all files bigger than 1000 lines with code maximally folded" or "open all files with top-level blocks expanded, but fold the rest" or something like that.