I do semi consider fight filler as reasonable canon as long as it doesn't conflict with any established rules, or is just poorly thought-out.
For instance, your Pein example. Although Deva controlling the rain was retconned when it was established that each body can only use ONE of the Rinnegan's innate abilities, which is where each Pein body derives it's name from. That means Deva also didn't use any of the other jutsus it appeared to perform while shown as a silhouette. And since Nagato was hidden in the same location when Deva did each of those things, it could be considered that Nagato just made it look like Deva used those jutsus in order to keep himself hidden; especially from us readers since it was a crucial plot-point.
Other feats, such as Tobirama's during his fight with Hiruzen, also seems fair-game to me, particularly since one of those two non-canon jutsus he used became canon and aren't haxxed.