I wasn't being able to find solution to this problem, so I decided to change strategy. Maybe someone will find it useful in he's situation.
I decided to split this query in two. So I'm using one query to select IDs for a limited subset of root entities and another to actually fetch whole tree by specifying retrieved IDs as a condition.
Example:
SELECT A.id
FROM Article A
LIMIT 10
SELECT A, C
FROM Article A
LEFT JOIN A.comments C
WHERE A.id IN (4, 8, 15, 16, 23, 42, ...)