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I found the menu responsible for this in the pin planner. According to "this page" (
https://www.altera.com/support/support-resources/knowledge-base/solutions/rd01112011_164.html) there is no way around this. Also there is nothing useful in the "pin connection guidelines" for cyclone5 devices..
So is there a way to remedy this?
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That indicates that before a device is configured, and during configuration, the weak pullups will be enabled on the I/O pins. However, you can configure the I/Os to have no weak pullup and no bus hold, so a output that is disabled will only source the leakage current (between -30uA and +30uA per datasheet). BTW 30uA at 3.3V is about 110K effective ohms (minimum; will be higher for lower currents) so even with the weak pullup disabled there will be a pullup/pulldown of something on the order of 110K to 220K or so ohms per I/O.
Picture of the I/O structure:
https://alteraforum.com/forum/attachment.php?attachmentid=15362&stc=1
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