My heart says that overclocking IP is a fun little game-within-the-game that adds some drama and excitement to close races, so my first choice would be to stick with status quo.
However, since Niv is opposed to the practice, it seems to me that the most effective, least disruptive way eliminate it is to simply cap the points that any team can earn from IP. In FGPTS, where each IP is worth +7.4 points, this would mean each team would be capped at 11,100 points from that category. Nothing else needs to change.
The reason this would work is that except for a small handful of elite pitchers (who will almost never be available to acquire late in the season) if we disregard the points earned from IP, the aggregate of everything else pitchers do contributes negative points. This is apparent at a glance by observing how few pitchers earn more than 7.4 P/IP overall. (I don’t know how this looks in SABR Points, but I suspect it’s similar.) If the software deprives teams of the points for IP, but allows them to earn points (positive and negative) from K, HR, BB, etc., any team that goes past the soft cap of 1500 IP is more likely to lose points than gain them as a result of going over.
This wouldn’t remove the ability to blow past the soft cap. It would remove the incentive to do so.