Take a look at this screenshot: http://prntscr.com/cakr8t
Given that each goal gives the same $ value and the cost per visitor is different (in this case, the total cost of 4362 visitors in group A is the same as the total cost of 2755 visitors in group B), then we're not able to use the calculator to make statistical decision.

What is the workaround to tackle this problem? Is there a way to incorporate the cost in this calculator? Or there is an entirely different method to look at this data.

Can you provide more details on the problem you're trying to solve? If 39 is some measure of cost per visitor, it wouldn't be appropriate to enter it in that calculator; rather you would need to enter the number of visitors that meet some criteria (or goal, using the website's nomenclature).