Whether you keep your breasts will be largely down to genetics and a bit of luck but there are a number of women i have advised as below who have trimmed down most places and either kept or increased cup size. A few others have dropped a bit but not enough for them to worry about. Like it or not they are bags of fat and as such there is an element of chance, everything else is certain if you are sensible.
Disclaimer done here we go.
Step 1. Ditch the whey protein or other supplements unless you know there is a particular dietary issue that you need to treat, inability to absorb iron etc.
There is a key word there 'supplement' if your diet is right you don't need to supplement it. A simple truth hardly anyone relly believes until they have done it.
Step 2. Ignore the scales. If the first one challenged your belief this one is going to seem less a step too far and more a leap of a cliff, but I can justify it. You are happy at your current weight but would happily lose a little, actually meaning your body shape is roughly what you want but you would like to be a bit leaner and more muscular. Toned does mean more muscular as it means you want your body to be fimrer and the only general tissue that is firmer than fat is muscle.
Because you will end up putting on muscle, allbeit in small quantities, you are likely to gain weight from this. If you lose fat too the chances are you may stay the same weight or even still get heavier while toning up. An old colleague of mine did incredibly well via commitment to diet and training and got down to the same weight as I have recently gone up to. Side by side we were the same height but he was visibly bigger than me. He was in better shape than many but I have decades of training behind me meaning I may be ugly but I am still muscular and relatively lean. Weight is the least accurate measure please avoid obsessing over it, as much as you can if seeking aesthetic changes, use the mirror as your guide, this is not easy.
Step 3. Balanced diet. I don't do macro level nutrition because having studied down to it I realised it's mind-numbingly complex and absolutely impossible to guarantee getting right. Once you accept that diet will never be 100% correct you realise high level is the best place to manage it from. This is why I direct people to the food pyramid as a guide on proportion, not number of portions. If you try to do x servings of y etc. you get confused on what is a serving etc. Just look at the size of the section and have that for your diet. Mostly complex carb aka staple food like rice, pasta, potatoes and bread, sensible fruit and veg which due to their size will actually give little in calories compared to everything else but bulk out the meal, moderate meat, fish, dairy and very little in the way of treats, sauces, oils processed dairy (butter etc.) and sugars.
Eat what you need volume wise. If you want to lose weight and keep figure only reduce by very small amounts across the board. Fat loss will be very slow but there is no rush.
Step 4. Training. The link you were given by plugeye is a good one, I have used it many times. As Justin said you need to have variety regarding intensity to have cardio at the low end and other training at the high end. You like pilates which will compliment what I am going to suggest well as the stretches will reduce aching and risk of injury.
Toning reps I would normally put at around 12 to 20 per set, so the workout goldfish has set up in the artical from plugeye using a rep range like this would tone you up nicely. However in my experience women doing heavier weights tended to build a bigger bust over half the time, stay the same most of the rest and lose rarely. As such I would say sets of 10 or 12 reps would likely suit you best. This carries a risk because the lower rep range you are doing the higher weight you should be using to ensure overload, higher weight brings with it higher risk of inury through incorrect movement, so only do this once you are totally confident with every exercise. If you start doing 15 or 20 a set to get used to it then shift to doing 10 and 12 a set a few months later you will gain far more than if you damage yourself going too far now.
Make sure you do your cardio, the heart and lungs are rather more important than how round your butt is, so don't forget this bit. If you enjoy going on a run, or cycle several times a week great, do it and nice to know there are others as sad as me. If not use aerobic classes or circuits, anything that keeps your heart rate elevated constantly for a duration of at least 20 minutes is ideal, there are alternatives, many do work but this keeps things simple.
Keep the pilates and ideally do some of the stretch movements at the end of every workout. The benefits of flexibility are many covering injury avoidance etc. Besides which there is nothing more pathetic than someone who is picture perfect but can't move.
Step 5. Final and most important. Find stuff you enjoy. If you try what I have said and hate it, come back and complain. We will not only give you your money back but will suggest alternatives based on your feedback. If you hate it even after giving it a chance stop it. If you perservere you will be deferring the inevitable stop. Almost without fail, those who hate what they do stop, those who love it continue. It is better to do something you love that takes a year or more to get what you want now than something you hate that takes months. Because you will have new targets in a year or so and only by doing stuff you love will you want to continue toward them.
I will gaurantee you everyone here who has achieved what they want thoroughly enjoy what they do. We enjoy different stuff but none of us care about that.