I wouldn't swim with the penguins in winter (June/July, as it is very cold then! Although the Indian Ocean (Fish Hoek, Simon's Town side) is warmer than the Atlantic Ocean (Hout Bay, Clifton Beach and Camps Bay Beach side).
Imhoff is OK, has some nice cheese and arts and crafts... if you enjoy browsing then it's lovely to visit.
The camels do not ride on the road, but on the beach, which is lovely. I do recommend this. There are places there to horse ride on the beach too (Long Beach, Noordhoek).
For Ostriches I would venture to Oudtshoorn, which is a bit far out of Cape Town... but I would not condone riding an ostrich, it is NOT healthy for them at all, no matter what people say. It does a lot of damage to their legs.
Winter weather is not great in Cape Town, if it were only cold that would be fine, unfortunately Cape Town gets cold, wet and windy... so let's hope for a mild winter whilst you are there! The cold is chilly but not as cold as other places in SA, like Joburg (inland and on the Highveld).
Car rental is definately best, get a car at Cape Town International. Alamo are a good hire company, inexpensive and we have used them a couple times when we have been back on holiday.
www.sleeping-out.co.za is quite good, as is Rooms For Africa, here is a link to cheap accomm there.
http://www.roomsforafrica.com/dest/south-africa/western-cape/cape-town.jsp?filter=3&sort=4&x=10&y=13
If you have more questions, please do feel free to ask. Happy planning! :)

