Of course you'll bring seed and likely animals too. People like familiar foods and replicators are known to crank out food that tastes "off."
No one is suggesting moving an intelligant species to the side, but replacing a regions native animals or plants? Yes please.
Growing flora and fauna does not require a powerful energy source, a replicator does. Animals naturally replace themselves and increase in numbers too.
The idea for landing the transport ship is a good idea, unless your intent is for it to make multiple trips bringing waves of colonists over time. The first wave prepares the site, creating roads, water reservoirs (hydro power maybe?), the first towns, etc.
Second and subsequent waves arrive at a measured pace, as the colony can absorb them.