The problem hasn't started now; it's just the consequence of the earlier step you took. If you were in your manager's position, what would you have done? I guess the same thing he is doing now, and almost for the same reasons, right?
Addressing Your Queries
Regarding the 1-year moral agreement, one year is not a significant period in the IT sector. Unless you have very specific reasons why you don't find this agreeable, just go with the tide.
As for your 'condition' about a salary hike/raise, I suggest not putting this as a sort of condition. At this point, you are in no position to impose any conditions. Ask your manager whether you would be eligible for any hikes during the year if your performance is good or better than it has been so far. Present it as if you are seeking clarification on this point, as you don't want any situation later where you are not given a raise due to this resignation issue. Ask what you want, but with a shift in the 'how.' Hope you get the point.
If possible, try to get this in writing (I know it could be tough) when HR accepts your resignation withdrawal. This is to preempt any future situation where your manager himself may leave the company, and HR may say they don't know anything about what he said regarding the hikes. If writing is not possible, then let this be discussed in front of the HR person.
But if you are asking for the raise now, I don't think that's realistic or fair. What you are doing now is correcting your mistake, not negotiating for a counter-offer.
Finally, regarding your remarks about being punished for being honest, I would still say, "Honesty is the Best Policy." Just keep it up; no one has ever regretted being honest in the long term.
All the Best.
Regards,
TS