Would Maeguiars Scratch X 2.0 be too strong for the paint of the bicycle? Or should I use something else to remove the scratches? Also I've heard that you could use the scratch remover to blend in the touch up paint (enamel) that you just applied to blend in with the original one.

I would start with something safe for clear coated paint, thats usually pretty mild. I f the scratch it through the clear coat but the color still remains then I normally would put a clear coat over the scratch, wet sand with a fine paper, 800 or 1000 grit and add clear coat until the scratch was level. then a little rubbing compound to polish it up.
Alot depends on what is on the bike to begin with too.

I used Turtle Wax liquid rubbing compound on my two older bikes when the paint started to get dull and now they are bright white, just like new. Hard to see swirl marks on white but they did have some small black marks and scratches that I could never get off and the rubbing compound did the trick. Then of course I waxed the paint afterwards. I also used it on my 21 year old MTB and now it's gleaming. I would try some rubbing compound first, it will not hurt the paint.

OP,
You need to be more specific about your particular bike and paint job. A pic would help. Matte finish bikes for example can be a disaster with any fine polishing compound.
If a gloss finish, you have a lot of options. Post a picture of the scratch if you want the best answer and technique.