Is it Ok to leave it like this, or should I avoid it. And if I should, how can I done it in Eagle?
Since your ground pour has the same net name as GND, when you
ratsnest the GND traces will disappear (be "consumed"). If you want them separate you'll have to name your ground plane something else and connect it with a cap or 0R resistor (or even a ferrite bead if noise is a problem). I do this on some power planes to isolate them (AGND, GND, CGND, etc). You can leave it if you aren't concerned with keeping them separate.
On boards (or traces) where it isn't a concern to me, it is helpful because I don't have to be concerned about routing ground traces. The only time you have to route them is if you have an isolated pour or your DRC settings don't allow the pour to get to your pin.