The A14 is to bypass having to drive through the already congested town centre. The current rail line through Ipswich doesn't have that problem.
Given that there's no pressing need for the line to go South of the town centre, it's far easier to go on the flat(ish), North of it, than it is to build a relatively huge bridge.
Thanks for the two replies. You gather I was just looking at a map. Incidentally, I did not realise it was hilly south of Ipswich. I once went to Harwich for the ferry and thought it was flat around there. Also by the way, I was not envisaging following the A14 to the west of Ipswich from Felixstowe but joining the line through the station area northwards to rejoin the line near the bacon factory, but perhaps it would make it too congested there?
I've had a look through Street View now and see the point, although a swing bridge perhaps might have been used (beware drunken Russian skippers though).