How to rejoin the College of Winterhold if Ancano is hostile

The game can be played any way you want, but some of the advantages of visiting the College of Winterhold are:

• Access to spells: spells from all schools of magic can be bought there
• Mage-friendly quest rewards: you'll get quite a few nice mage-centered quest rewards, like the Archmage robes and the Morokei mask
• Access to trainers: if you feel like paying for training, the high level mage trainers are mostly (all?) in the College of Winterhold

It is a long way, but you can easily travel there using a wagon. If you're following the main quest line, once you get to Whiterun you can take a wagon from in front of the stables.

So, I would recommend traveling there shortly after you reach Whiterun. After getting Lydia or after visiting the Throat of the World seem like good times to peel off and do the mage quests.

She may have gotten herself lost during the commotion. Settle your bounty and wait a day or two away from Winterhold, then come back during business hours (just to be safe). If that doesn't help, follow Halfwarr's advice.