Pull-ups/Pull-Down/Slew-Rate I/O pins definitions

There is no after user mode state normally, unless you reset the configuration by asserting nconfig or reprogram the device through JTAG. The weak pull-ups are provided by Altera to assure defined behaviour and avoid excessive current consumption of input drivers caused by floating pins with mid-scale input voltage. They can't be changed.

The only disadvantage of weak pull-ups is, that you need a 2k2 or below external pulldown for an output, that must be assured to stay at low level in unconfigured state. So, for a low power design, it may be meaninful to use an external inverter instead.