You CAN fire directly if you have the crews 'indirect fire' upgrade.
The crew are trained to fire indirectly. The gun is not modified or changed in any way, so the ability to fire directly remains. If someone tried to get under the Basilisk's indrect range and then tricked you into believing you could not attack them, they are a cheat.
The Codex does not define this very well. You should try to bear in mind that unless the Codex specifically states that you CANNOT fire directly with an upgrade, then the original skill remains.
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