Wow, aches... yes I think they happen to all of us now and then. I know I recently really upped my lifting routine with some weighted lunges and squats. OMG, for the three days following my routine I had trouble sitting and walking; I think I over did it.
You've been aching everyday for 2 weeks? If you're changing your pilates workout every time then I wouldn't think this is too outrageous. If you're doing the same workout everytime though, I'd think the aches might be a sign that you're overdoing it just a tad. You say you haven't worked out in a long time, so some soreness is expected. In my opinion, however, 90% of that achiness should be gone before you workout again. Remember that you need to give your body some time to heal!!!
I know it's really difficult to balance the sometimes hard to come by motivation to work out with realistically taking days off, but occasionally it's necessary. I personally don't lift weights until I am completely healed up from the previous session. This usually takes 1-3 days. The way I work around this is I do my lower body on one day, my upper body on the next, and my stomach/core on the third... by the day after my core my legs/glutes are usually fully recovered and I start the cycle again. I'm not very well versed in pilates but you may find this sort of routine helpful if it's possible... focus on one area each day and alternate areas so that your muscles get a full shot at recovery yet you still are able to stay in the swing of working out daily.
There are some other small things you can do to promote healing. Make sure you're drinking your water!!! Staying hydrated is very important and almost every intensive training program requires a daily intake of 8 glasses. Even the Army MAKES its recruits consume their 8+ glasses of water a day during basic training. It's that important!
Also, try to keep focused on eating a healthy, well-rounded diet. Are you getting enough carbs and protein? These are resources that your body needs to properly rebuild.
And lastly, there is such a thing as too much/over-training. Only you can examine your situation honestly and decide if you think your body needs a day off. If you're constantly sore you may want to put the pilates on hold until you heal up. This may take a few days, and during that time if you're concerned about losing your motivation or progress you can always increase your walking time to compensate.
Either way, don't fret and don't get discouraged!!! The key to getting to your ideal weight is finding what works for YOU. They'll be many moments when you find you have to taper your eating/exercise routine up or down, one way or another. I think it's very important to be flexible with your routine and goals. Remember that while you're on this weight loss journey, you're still living your life... and you have to find a way to incorporate your exercise and such into your life without making yourself miserable
You will get there!
I hope something I've said helps! Best of luck to you and congratulations on an excellent and solid start to improving your fitness!!!