Say I get Malekith into a unit with a magic standard carried by a regular standard bearer (not the BSB). I have Malekith in base to base with the standard bearer, could I use Malekiths ability to destroy this item?

I am leaning towards yes as I would target the rank and file troops and they just so happen to have a magic item. I am a bit biased on this though so thought I would look for a second or third opinion.

You can only divide attacks between different enemies in close combat if they are legal targets for the attacking model (i.e. in base contact or in position for a supporting attack) and have different profiles - BRB p48, "Dividing Attacks". In the example above, if the unit had a champion or contained a character, and if the standard bearer and that other model were both in base contact with Malekith, he could split his attacks between the standard bearer (as a rank and file member of the unit) and the champion or character.

Where it gets confusing is whether you can destroy items with Destroyer in this situation. Standard bearers cannot be removed as casualties except as provided at page 94 of the BRB. However, that section states that "We assume that if the standard bearer is slain, another warrior will step forward to raise the fallen standard aloft." This clearly contemplates that the standard bearer model can be separately attacked - it's just that killing them won't remove the standard from the unit (it may help to think of it as a Look Out Sir!-type effect which always works).

Given that the BRB seems to contemplate that the standard bearer could be separately attacked, as long as the requirements for being able to divide attacks were met, there's a good argument that Destroyer could knock out a magic standard in this situation. However, if your opponent is... resistant to this reasoning, you can always fall back on the 1-3/4-6 rule for deciding whose interpretation applies.

That's the answer I was looking for

Couple all that with the line in Malekiths entry that states all enemy models in base contact must reveal their magic items. It does not limit this to characters and so makes any model a target for the Destroyer. Most of these targets just don't have any magic items so it isn't usually an issue.