I believe this is largely an API design problem. Many client APIs (especially ORMs) will start a transaction implicitly for you if you haven't explicitly specified your own, leading to problems like in the article.
Having implicit transactions is just wrong design, IMO. A better-designed API should make transactions very explicit and very visible in the code: if you want to execute a query, you must start a transaction yourself and then query on that transaction supplied as an actual parameter. Implicit transactions should be difficult-to-impossible. We - the programmers - should think about transactions just as we think about querying and manipulating data. Hiding from transactions in the name of "ergonomy" brings more harm than good.
This means that the transaction becomes its own block, clearly separated, but which can reference pure values in the surrounding context.
do
…
some IO stuff
…
res <- atomically $ do
…
transaction code
which can reference
results from the IO above
…
…
More IO code using res, which is the result of the transaction
…