The Dalek who saw Adelaide and recognised that her future included a fixed point may well not have known about the plans for the "reality bomb". It was just an ordinary soldier and the high command (in any army) very often doesn't tell the ordinary soldiers what the plans are. On the other hand, Davros, the Supreme Dalek and others who did know about the plans for the "reality bomb", didn't themselves encounter Adelaide. Among the Daleks, therefore, different individuals would have had different parts of the picture but no one individual would have had all of the picture. That kind of thing happens a lot.
Another possibility is that the Dalek who saw Adelaide did know of the "reality bomb" and left her alone because it thought that interfering with a fixed point would risk messing up the over-all plan. Perhaps their failure was not a fixed point and was in flux (after all not every important event has to be a fixed point in time). We saw in "The Wedding of River Song" just how drastic a mess interfering with a fixed point can cause. The Dalek may simply have decided that killing her then wasn't worth the risk, especially as (so far as it knew) she'd soon be dead, anyway. In other words: if the universe survived, Adelaide had to survive; if the universe was destroyed, it presumably wouldn't matter either way; therefore, the only sensible thing to do was to let her live.
We don't know enough about what individual Daleks did and didn't know to be sure which explanation is the right one.