Barrels aren't supposed to be pitted from the start. Sorry...that to me is unacceptable. You can call H&R and discuss what you have done and see if they issue you a call tag to return it to them. I don't know if they will be able to do anything since your 2" groups is within the factory acceptable range.
If you elect to keep it,check the FAQ's for some quick and easy ways to touch up the crown on the rifle. This can and will effect your groups. While in the FAQ's look at all of the other tips for getting the best accuracy from your rifle. Contrary to many here, I shoot with a clean barrel when shotting for groups.If a rifle barrel won't shoot good when clean,there is something wrong with it.These barrels can be exceedingly accurate and you will note everyone has their own technique for getting the most from them. Some fundamentals for shooting them is universal,no matter what and that is having a smooth but complete trigger pull on each and every shot. This is one thing those who aren't used to shooting a single shot break action have the greatest issue with.Transitioning over to a shotgun type trigger from a true rifle type trigger is something a person needs to practice doing,and it isn't easy if you have been shooting most bolt actions for the longest time,so it is something many fail to do.
Bedding the forearms is another thing many have had luck with doing various ways. A simple o-ring used starting off seems to help the majority of people instead of a full hard bedding job.The reason is these rifles are not like a bolt action receiver at all in regards to how they best preform. This is due to the variances each Handy Rifle has. No 2 barrels are exactly fitted the same,since each is hand fitted and there are differences in the depth of the the barrel lug and it's position where it is mounted on the barrel.This is easily seen when switching factory fitted barrels in the position where the barrel screw stud is in the same forearm.Many will be real close to the same place,many won't be and will be tighter or looser.This is why experimenting with the forearm tightness is important. You can tighten up or loosen up the fit somewhat of the barrel to the receiver by adjusting the tightness or looseness of the the forearm. Just look at how the barrel fits into the receiver and then how the forearm effects it when to take it apart and put it back together.
I've tried many different ways of fitting/bedding the forearms.From just doing a simple o-ring on the barrel screw stud,to drilling out the forearm and installing a brass insert so I have metal to metal contact,and then doing a full skim coat of bedding and even adding powdered stainless steel to the mix. I've also completely free floated the barrel channel to doing nothing with else with them and just use a o-ring on the barrel screw stud.Lately I have been opening the barrel channel completely allowing 1/16" to 1/8" gap all the way around then doing a full soft bed of RTV silicon bought at Auto Zone in a tube.This has given me my best shot to shot consistency of any treatment I have used provided I torque the screw down the same each time I have removed the barrel.
I don't know if any of what I do will help you,it may or may not.Like I said..we each have our on way of doing things,and sometimes it runs counter to what the rest of the herd is doing.You can experiment some more or call them and ask about send it in. If you keep it,there are ways of shooting it with special treated bullets to remove the pitting completely,but it does wear the barrel down in doing so and could effect the shooting life of it.There are many pro & cons from dozens of places about doing this.The name of the product I am referring to is Tubb's Final Finish kit.
Do check the OAL of your chamber to get a idea of where you should seat your bullet depth..this is critical to do,since chamber dimensions do vary from barrel to barrel,and should be a standard practice for any one who reloads their own ammunition.Tweaking your rifle to produce sub moa groups or even consistent groups can be at times a very time consuming process...Many times we get lucky many other times we don't and think we should have a super accurate rifle from the get go with any Handy,and it doesn't always work out to be that way.
Good Luck
Mac