You're making a hash of leverage, margin, risk, the 2% rule, and margin calls. Let's try to sort it out.
50:1 refers to leverage, not margin.
The margin percentage corresponding to 50:1 leverage would be 2%. This 2% required margin percentage has nothing to do with the 2% rule you are asking about.
The 2% rule refers to risk as a percentage of account balance.
Risk is defined as the loss (in pips or in dollars) that would occur, if your position is stopped out.
Let's use an example to illustrate risk.
Let's say you open a 1-micro-lot position in GBP/USD, and let's say that you place a 35-pip stop-loss on this position. We know that each 1-pip move in this position is worth $0.10, because that is true for all 1-micro-lot positions in pairs of the form XXX/USD. Therefore, the dollar-risk associated with your position is 35 pips x $0.10 per pip = $3.50.
Your dollar-risk was determined by (1) the pair you traded, (2) the size of your position, and (3) your stop-loss. Your account leverage and your account balance had nothing to do with this calculation of risk.
If your account balance happens to be $1,000, then we can calculate that your risk ($3.50) is 0.35% of your account balance.
Suppose you want to apply the 2% rule. This rule states that your risk (at stop-out) should be 2% of your account balance (not 0.35%, as in the above example).
In order to increase your risk to the 2% level desired, you must increase your position size. This is tricky to calculate by hand, so it's fortunate that there are Position Size Calculators for this purpose. Babypips has a good one.
You enter the metrics for your trade into the Position Size Calculator, click Calculate, and you get this:
The Calculator is telling you that your specified risk percentage (2%) and your account balance ($1,000) combine to yield a risk amount of $20.
And, given your specified 35-pip stop-loss, the position size that corresponds to that exact risk amount is 5,714 UNITS of GBP/USD.
What if your account does not allow you to trade in individual UNIT amounts?
Then, you will have to scale back the size of your position to 5 micro-lots (which is only 5,000 UNITS). You can't scale up to 6 micro-lots without exceeding your 2% risk rule.
If you adjust the size of your position down to 5 micro-lots, what will your actual risk percentage be?
Actual risk percentage = 2% x (5,000 / 5,714) = 1.75%.
And that's as close as you can get to the desired 2% risk, without exceeding it.
I hope that clears up your confusion,