Charlie,
No, it won't hurt anything, actually if you run low on space, the updater will prompt you that space is needed. You'll have several options like to remove Alaska data, a Particular region, IFR, etc. Typically if you don't plan on flying to Alaska, delete it, you can always grab it later.
Also, you can get a larger SD card and copy/paste all contents (except iFly Streets folder) from your original card to the new larger card. Just beware, iFly Streets is bound to the original card and will not work on the larger card so you'd need to keep the old card for Streets use. I hope this helps.