According to the Pathfinder SRD site,
These bonuses can be added to the weapon, stacking with existing weapon bonuses to a maximum of +5
So you can take the +1 weapon after the Magic Weapon spell, and add up to +4 worth of bonus to it from the Bond. So you won't supercede the bonus until level 17, where I imagine you'll have much better than just a level 1 Magic Weapon spell.
EDIT: I forgot to address the DR question. In which case I reference:
Any weapon with at least a +1 magical enhancement bonus on attack and damage rolls overcomes the damage reduction of these monsters.
Also just to have the full ability written out:
At 5th level, this spirit grants the weapon a +1 enhancement bonus. For every three levels beyond 5th, the weapon gains another +1 enhancement bonus, to a maximum of +6 at 20th level. These bonuses can be added to the weapon, stacking with existing weapon bonuses to a maximum of +5, or they can be used to add any of the following weapon properties: axiomatic, brilliant energy, defending, disruption, flaming, flaming burst, holy, keen, merciful, and speed. Adding these properties consumes an amount of bonus equal to the property's cost (see Table: Melee Weapon Special Abilities). These bonuses are added to any properties the weapon already has, but duplicate abilities do not stack. If the weapon is not magical, at least a +1 enhancement bonus must be added before any other properties can be added.
Therefore, whatever the final +X bonus comes out to be is the DR bypass.
Frankly,
Do it with skill checks and keep it out of combat, there is no combat mechanic for controlling an army because 4e is dependent heavily on the action economy that would break hard by giving a PC multiple undead allies with their own actions.
Basically, the tactical combat play in 4e is reliant on balance, and what your proposing will break the balance, hard.
However, let's talk about the skill check option here. What your opening up is the potential for a couple of sessions of largely narrative play. It will primarily involve skill checks and challenges and is a huge opportunity for your players to embrace the role playing aspects that 4e does actually do quite well.
However, for this, you're going to have to throw the combat aspects of the rule book out the window and go with your imagination and story telling aspects. There are explicit not rules for this (intentionally so), instead there is the skill system, which you can use to support the narrative play that is called for here. So develop some skill challenges that fit and have a good idea of a couple of different plot threads that you could take and then see where your players and rolls take you.
If you want the actual mechanical guts of this: the sword provides the location of the ritual (make it up) and a short skill challenge with religion checks (easy DCs) should get him a decent army depending on his checks, after that, what he does with it should be a series of narrative cut scenes, your end goal should be to advance the character, but if you want to continue the game as a traditional 4e exercise you've got to get him back to just being him.
Best Answer
Yes.
The only indication of what the bond applies to is this:
Nowhere does it indicate that the weapon must be designated ahead of time.
More importantly, no provision is given for upgrading weapons, something that would be extremely important to detail if the bond was permanent/semi-permanent.
Of course, you could roleplay your paladin as the type who obsessively uses a single weapon (this is my sword). But you can also roleplay him as someone who turns whatever weapon is at hand into an instrument of divine might.