This is very similar to this question.  Here's a modified version based upon sris's answer:
paths = [
  "nodeA1",
  "nodeA1/nodeB1/nodeC1",
  "nodeA1/nodeB1/nodeC1/nodeD1/nodeE1",
  "nodeA1/nodeB1/nodeC2",
  "nodeA1/nodeB2/nodeC2",
  "nodeA3/nodeB2/nodeC3"
]
tree = {}
paths.each do |path|
  current  = tree
  path.split("/").inject("") do |sub_path,dir|
    sub_path = File.join(sub_path, dir)
    current[sub_path] ||= {}
    current  = current[sub_path]
    sub_path
  end
end
def make_tree(prefix, node)
  tree = ""
  node.each_pair do |path, subtree| 
    tree += "#{prefix}<#{File.basename(path)}"
    if subtree.empty?
      tree += "/>\n"
    else
      tree += ">\n"
      tree += make_tree(prefix + "\t", subtree) unless subtree.empty?
      tree += "#{prefix}</#{File.basename(path)}>\n"
    end
  end
  tree
end
xml = make_tree "", tree
print xml
Edit:
Here is a modified version that builds an actual XML document using Nokogiri.  I think it's actually easier to follow than the string version.  I also removed the use of File, because you don't actually need it to meet your needs:
require 'nokogiri'
paths = [
  "nodeA1",
  "nodeA1/nodeB1/nodeC1",
  "nodeA1/nodeB1/nodeC1/nodeD1/nodeE1",
  "nodeA1/nodeB1/nodeC2",
  "nodeA1/nodeB2/nodeC2",
  "nodeA3/nodeB2/nodeC3"
]
tree = {}
paths.each do |path|
  current  = tree
  path.split("/").each do |name|
    current[name] ||= {}
    current  = current[name]
  end
end
def make_tree(node, curr = nil, doc = Nokogiri::XML::Document.new)
  #You need a root node for the XML.  Feel free to rename it.
  curr ||= doc.root = Nokogiri::XML::Node.new('root', doc)
  node.each_pair do |name, subtree|
      child = curr << Nokogiri::XML::Node.new(name, doc)
      make_tree(subtree, child, doc) unless subtree.empty?
  end
  doc
end
xml = make_tree tree
print xml
Edit 2:
Yes, it is true that in Ruby 1.8 hashes aren't guaranteed to maintain insertion order.  If that's an issue, there are ways to work around it.  Here's a solution that retains order but doesn't bother with recursion and is much simpler for it:
require 'nokogiri'
paths = [
  "nodeA1",
  "nodeA1/nodeB1/nodeC1",
  "nodeA1/nodeB1/nodeC1/nodeD1/nodeE1",
  "nodeA1/nodeB1/nodeC2",
  "nodeA1/nodeB2/nodeC2",
  "nodeA3/nodeB2/nodeC3"
]
doc = Nokogiri::XML::Document.new
doc.root = Nokogiri::XML::Node.new('root', doc)
paths.each do |path|
  curr = doc.root
  path.split("/").each do |name|
    curr = curr.xpath(name).first || curr << Nokogiri::XML::Node.new(name, doc)
  end
end
print doc