As you have seen, then no that would not be the easiest way to do things. Basically you made a mistake in using these pins in the first place. Just swallow that fact and rearrange those pins so they are not used for something else.
Using software I2C drivers are a poor choice because they don't always work on the full I2C specification. First they are slower and second they don't always have the same pulse stretching capabilities a real I2C circuit has.
The alternative is to use a processor that's got two I2C busses in the first place.