Well, its the same problem we've always faced even with just the Pearl Quest or any Side Quest vs. only doing a Pirate with weapons like you, I and a few others have done: we know that free REP drains away damage to weapons - the question becomes is the entertainment value worth it...
In this case I believe its ok for the higher levels - only because of the 2 factors which Ironhawks chart shows us to calculate the levels (Noriety REP + Weapon REP / 2)
(See Ironhawks awesome Chart Guide Here). If I am a Level 35 with a Level 20 Sword ( or in numbers 35+20=55/2=27.5 rounded up = 28 and after a few battles I hit 36 ( 36+20=56/2-28) it made no difference at all... I still need L28 or better enemies to get the best REP score. In the 40s it would take several invasions just to change one of those numbers - so there no worry there.
The lower levels do take a hit, but unlike the much larger Pearl Quest the hit is not nearly as large. If I'm 25 with a Sword of 9 to start (24+9=34/2=17) and after a few rounds I'm Level 26 with a sword of 11 (26+11=37/2=18.8 rounded to 19) it does mean I need L19 enemies to get max REP - but many enemies can still be found for my L26 guy to kill at L19.
The only thing I would be careful of is the weapons balence as EX mentions - its too tempting to favor one weapon and ignoring the others for battles (hence if I get 4 noriety to get from L21 to 25 that day but my pistol is still only level 5 - beating higher level enemies with a L5 pistol will be a pain).
Does this mean lower levels should not do invasions? I don't think so - feel free to join in

, because a) if they are somewhat careful to keep balenced weapons they can mostly keep their REPs good and b) the real issue of being more entertained (instead of just weapon grainding all day) more than justifies a bit of hard work that may be required
(There will always be players who just jump on for the invasions and jump off though - they will have to deal with levelling on their own terms though

)
In the end - its a very good point Basil and a good reminder to everyone that though invasions are fun, always be working all your weapons (espically thouse you don't use during invasions during the off times) and levelling when you can so as not to throw off your pirates balence too much