Still fight for one side or the other after forging the truce in “Season Unending”

Achievements Unlocker mod can unlock all achievements or any achievements you choose with a little Creation Kit modification (Available through Steam -> Library -> Tools). You can also use Steam Achievement Manager to add or remove any Steam achievements. All in all, these options are likely much faster and less bug-prone than messing around with using console to trigger alternative missions.

Answer to this is Probably Not

Aela has a strong loyalty to Jorrvaskr. Which has its loyalty to the Imperials. If the Imperials win then Vignar Gray-Mane is the new Jarl of Whiterun.

She is part of many factions but these are of importance :

1. GuardFaction (makes an actor a guard)
2. PotentialMarriageFaction
3. TownWhiterunFaction

She is part of Town Whiterun faction and Guard faction. Which automatically makes her not available for marriage in your case, since entire of Whiterun will not have Whiterun guards. They are replaced by Stormcloak soldiers.

Also according to her entry at UESP:

Aela is part of the Guard Faction. There is a bug wherein due to being part of the Guard faction, Aela may behave erratically if she's following you when beginning the Battle For Whiterun quest.

According to entry for Battle For Whiterun at UESP Stormcloak version:

Also during Battle For Whiterun (Stormcloak version), Aela the Huntress may disappear if she is your wife at the time. She may come back eventually after you moved on to the next Quest, Liberation of Skyrim.

Since you have completed Liberation of Skyrim quest and still can not find Aela, you probably might not be able to marry her.